BLAST/PSI-BLAST
Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J.,1997.
Gapped BLAST and PSI-BLAST : a new generation of protein database search programs.
Nucleic Acids Res. 25,3389-3402.
Reverse PSI-BLAST
Marchler-Bauer A, Panchenko AR, Shoemaker BA, Thiessen PA, Geer LY, Bryant SH., 2002.
CDD: a database of conserved domain alignments with links to domain three-dimensional structure.
Nucleic Acids Res 30, 281-283.
SOSUI
Hirokawa T., Boon-Chieng S and Mitaku S., 1998.
SOSUI:classification and secondary structure prediction system for membrane proteins.
Bioinformatics 14, 378-379.
MULTICOIL
Wolf E., Kim P.S., Berger B., 1997.
MultiCoil:A program for predicting two- and three-stranded coiled coils.
Protein Science 6, 1178-1189.
SEG
Wooton J.C., Federhen S., 1996.
Analysis of compositionally biased regions in sequence databases.
Methods Enzymol. 266, 554-571.
Genomic Sequence(Archaea)
Aeropyrum pernix
Kawarabayasi,Y., Hino,Y., Horikawa,H., Yamazaki,S., Haikawa,Y., Jin-no,K., Takahashi,M., Sekine,M., Baba,S., Ankai,A., Kosugi,H., Hosoyama,A., Fukui,S., Nagai,Y., Nishijima,K., Nakazawa,H., Takamiya,M., Masuda,S., Funahashi,T., Tanaka,T., Kudoh,Y., Yamazaki,J., Kushida,N., Oguchi,A., Aoki,K., Kubota,K., Nakamura,Y., Nomura,N., Sako,Y. and Kikuchi,H.
Complete Genome Sequence of an Aerobic Hyper-thermophilicCrenarchaeon, Aeropyrum pernix K1 DNA Res 1999 Apr 30;6(2):83-101, 145-52
Sulfolobus solfataricus
She,Q., Singh,R.K., Confalonieri,F., Zivanovic,Y., Allard,G., Awayez,M.J., Chan-Weiher,C.C.-Y., Clausen,I.G., Curtis,B.A., De Moors,A., Erauso,G., Fletcher,C., Gordon,P.M.K., Heikamp-de Jong,I., Jeffries,A.C., Kozera,C.J., Medina,N., Peng,X., Thi-Ngoc,H.P., Redder,P., Schenk,M.E., Theriault,C., Tolstrup,N., Charlebois,R.L., Doolittle,W.F., Duguet,M., Gaasterland,T., Garrett,R.A., Ragan,M.A., Sensen,C.W. and Van der Oost,J.
The complete genome of the crenarchaeon Sulfolobus solfataricus P2 Proc Natl Acad Sci U S A 2001 Jul 3;98(14):7835-40
Sulfolobus tokodaii 7
Kawarabayasi Y, Hino Y, Horikawa H, Jin-no K, Takahashi M, Sekine M, Baba S, Ankai A, Kosugi H, Hosoyama A, Fukui S, Nagai Y, Nishijima K, Otsuka R, Nakazawa H, Takamiya M, Kato Y, Yoshizawa T, Tanaka T, Kudoh Y, Yamazaki J, Kushida N, Oguchi A, Aoki K, Masuda S, Yanagii M, Nishimura M, Yamagishi A, Oshima T, Kikuchi H.
Complete genome sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain7. DNA Res 2001 Aug 31;8(4):123-40
Methanosarcina mazei strain Goe1
Deppenmeier,U., Johann,A., Hartsch,T., Merkl,R., Schmitz,R.A., Martinez-Arias,R., Henne,A., Wiezer,A., Baeumer,S., Jacobi,C., Brueggemann,H., Lienard,T., Christmann,A., Boemecke,M., Steckel, S., Bhattacharyya,A., Lykidis,A., Overbeek,R., Klenk,H.-P., Gunsalus,R.P., Fritz,H.-J. and Gottschalk,G.
The genome of Methanosarcina mazei: Evidence for lateral gene transfer between Bacteria and Archaea J Mol Microbiol Biotechnol. 2002 Jul;4(4):453-61.
Haloarcula marismortui ATCC 43049
Baliga NS, Bonneau R, Facciotti MT, Pan M, Glusman G, Deutsch EW, Shannon P, Chiu Y, Weng RS, Gan RR, Hung P, Date SV, Marcotte E, Hood L, Ng WV.
Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Res. 2004 Dec;14(12):2510.
Halobacterium sp. NRC-1
Ng,W.V., Kennedy,S.P., Mahairas,G.G., Berquist,B., Pan,M., Shukla,H.D., Lasky,S.R., Baliga,N., Thorsson,V., Sbrogna,J., Swartzell,S., Weir,D., Hall,J., Dahl,T.A., Welti,R., Goo,Y.A., Leithauser,B., Keller,K., Cruz,R., Danson,M.J., Hough,D.W., Maddocks,D.G., Jablonski,P.E., Krebs,M.P., Angevine,C.M., Dale,H., Isenbarger,T.A., Peck,R.F., Pohlschrod,M., Spudich,J.L., Jung,K.-H., Alam,M., Freitas,T., Hou,S., Daniels,C.J., Dennis,P.P., Omer,A.D., Ebhardt,H., Lowe,T.M., Liang,P., Riley,M., Hood,L. and DasSarma,S.
Genome sequence of Halobacterium species NRC-1 Proc Natl Acad Sci U S A 2000 Oct 24;97(22):12176-81
Methanopyrus kandleri AV19
Slesarev,A.I., Mezhevaya,K.V., Makarova,K.S., Polushin,N.N., Shcherbinina,O.V., Shakhova,V.V., Belova,G.I., Aravind,L., Natale,D.A., Rogozin,I.B., Tatusov,R.L., Wolf,Y.I., Stetter,K.O., Malykh,A.G., Koonin,E.V. and Kozyavkin,S.A.
The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens Poc. Natl. Acad. Sci. U.S.A. 99 (7), 4644-4649 (2002)
Pyrococcus abyssi GE5 deltaH
Gaspin C, Cavaille J, Erauso G, Bachellerie JP.
Archaeal homologs of eukaryotic methylation guide small nucleolar RNAs: lessons from the Pyrococcus genomes. J Mol Biol. 2000 Apr 7;297(4):895-906.
Lecompte O, Ripp R, Puzos-Barbe V, Duprat S, Heilig R, Dietrich J, Thierry JC, Poch O.
Genome evolution at the genus level: comparison of three complete genomes of hyperthermophilic archaea. Genome Res. 2001 Jun;11(6):981-93.
Cohen GN, Barbe V, Flament D, Galperin M, Heilig R, Lecompte O, Poch O, Prieur D, Querellou J, Ripp R, Thierry JC, Van der Oost J, Weissenbach J, Zivanovic Y, Forterre P.
An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi. Mol Microbiol. 2003 Mar;47(6):1495-512.
Pyrococcus furiosus DSM 3638
Maeder DL, Weiss RB, Dunn DM, Cherry JL, Gonzalez JM, DiRuggiero J, Robb FT.
Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences. Genetics 152 (4), 1299-1305 (1999)
Thermoplasma acidophilum
Ruepp,A., Graml,W., Santos-Martinez,M.L., Koretke,K.K., Volker,C., Mewes,H.W., Frishman,D., Stocker,S., Lupas,A.N. and Baumeister,W.
The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum Nature 2000 Sep 28;407(6803):508-13
Thermoplasma volcanium
Kawashima,T., Yamamoto,Y., Aramaki,H., Nunoshiba,T., Kawamoto,T., Watanabe,K., Yamazaki,M., Kanehori,K., Amano,N., Ohya,Y., Makino,K. and Suzuki,M.
Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium Proc Natl Acad Sci U S A 2000 Dec 19;97(26):14257-62
Nanoarchaeum equitans Kin4-M
Waters E, Hohn MJ, Ahel I, Graham DE, Adams MD, Barnstead M, Beeson KY, Bibbs L, Bolanos R, Keller M, Kretz K, Lin X, Mathur E, Ni J, Podar M, Richardson T, Sutton GG, Simon M, Soll D, Stetter KO, Short JM, Noordewier M
The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc Natl Acad Sci U S A. 2003 Oct 28;100(22):12984-8. Epub 2003 Oct 17.
Genome Sequneces(Bacteria)
Corynebacterium diphtheriae NCTC13129
Cerdeno-Tarraga AM, Efstratiou A, Dover LG, Holden MT, Pallen M, Bentley SD, Besra GS, Churcher C, James KD, De Zoysa A, Chillingworth T, Cronin A, Dowd L, Feltwell T, Hamlin N, Holroyd S, Jagels K, Moule S, Quail MA, Rabbinowitsch E, Rutherford KM, Thomson NR, Unwin L, Whitehead S, Barrell BG, Parkhill J.
The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129. Nucleic Acids Res. 2003 Nov 15;31(22):6516-23.
Corynebacterium efficiens YS-314
Nishio Y, Nakamura Y, Kawarabayasi Y, Usuda Y, Kimura E, Sugimoto S, Matsui K, Yamagishi A, Kikuchi H, Ikeo K, Gojobori T.
Comparative complete genome sequence analysis of the amino acid replacements responsible for the thermostability of Corynebacterium efficiens. Genome Res. 2003 Jul;13(7):1572-9.
Corynebacterium glutamicum ATCC 13032(U.Bielefeld)
Kalinowski J, Bathe B, Bartels D, Bischoff N, Bott M, Burkovski A, Dusch N, Eggeling L, Eikmanns BJ , Gaigalat L, Goesmann A, Hartmann M, Huthmacher K, Kramer R, Linke B, McHardy AC, Meyer F, Mockel B, Pfefferle W, Puhler A, Rey DA, Ruckert C, Rupp O, Sahm H, Wendisch VF, Wiegrabe I, Tauch A.
The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins. J Biotechnol. 2003 Sep 4;104(1-3):5-25.
Streptomyces avermitilis
Ikeda H, Ishikawa J, Hanamoto A, Shinose M, Kikuchi H, Shiba T, Sakaki Y, Hattori M, Omura S.
Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis. Nat Biotechnol. 2003 May;21(5):526-31.
Tropheryma whipplei TW08/27
Bentley SD, Maiwald M, Murphy LD, Pallen MJ, Yeats CA, Dover LG, Norbertczak HT, Besra GS, Quail MA, Harris DE, von Herbay A, Goble A, Rutter S, Squares R, Squares S, Barrell BG, Parkhill J, Relman DA.
Sequencing and analysis of the genome of the Whipple's disease bacterium Tropheryma whipplei. Lancet. 2003 Feb 22;361(9358):637-44.
Aquifex aeolicus
Deckert,G., Warren,P.V., Gaasterland,T., Young,W.G., Lenox,A.L., Graham,D.E., Overbeek,R., Snead,M.A., Keller,M., Aujay,M., Huber,R., Feldman,R.A., Short,J.M., Olson,G.J. and Swanson,R.V.
The complete genome of the hyperthermophilic bacterium Aquifex aeolicus Nature 1998 Mar 26;392(6674):353-8
Bacteroides fragilis NCTC 9343
Cerdeno-Tarraga AM, Patrick S, Crossman LC, Blakely G, Abratt V, Lennard N, Poxton I, Duerden B, Harris B, Quail MA, Barron A, Clark L, Corton C, Doggett J, Holden MT, Larke N, Line A, Lord A, Norbertczak H, Ormond D, Price C, Rabbinowitsch E, Woodward J, Barrell B, Parkhill J.
Extensive DNA inversions in the B. fragilis genome control variable gene expression. Science. 2005 Mar 4;307(5714):1463-5.
Porphyromonas gingivalis W83
Nelson KE, Fleischmann RD, DeBoy RT, Paulsen IT, Fouts DE, Eisen JA, Daugherty SC, Dodson RJ, Durkin AS, Gwinn M, Haft DH, Kolonay JF, Nelson WC, Mason T, Tallon L, Gray J, Granger D, Tettelin H, Dong H, Galvin JL, Duncan MJ, Dewhirst FE, Fraser CM.
Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83. J Bacteriol. 2003 Sep;185(18):5591-601.
Chlamydia muridarum
Read,T.D., Brunham,R., Shen,C., Gill,S.R., Heidelberg,J.F., White,O., Hickey,E.K., Peterson,J., Umayam,L.A., Utterback,T., Berry,K., Bass,S., Linher,K., Weidman,J., Khouri,H., Craven,B., Bowman,C., Dodson,R., Gwinn,M., Nelson,W., DeBoy,R., Kolonay,J., McClarty,G., Salzberg,S.L., Eisen,J. and Fraser,C.M.
Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39 Nucleic Acids Res 2000 Mar 15;28(6):1397-406
Chlamydia trachomatis
Stephens,R.S., Kalman,S., Lammel,C.J., Fan,J., Marathe,R., Aravind,L., Mitchell,W.P., Olinger,L., Tatusov,R.L., Zhao,Q., Koonin,E.V. and Davis,R.W.
Genome Sequence of an Obligate Intracellular Pathogen of Humans: Chlamydia trachomatis Science 1998 Oct 23;282(5389):754-9
Chlamydophila pneumoniae AR39
Read,T.D., Brunham,R.C., Shen,C., Gill,S.R., Heidelberg,J.F., White,O., Hickey,E.K., Peterson,J., Umayam,L.A., Utterback,T., Berry,K., Bass,S., Linher,K., Weidman,J., Khouri,H., Craven,B., Bowman,C., Dodson,R., Gwinn,M., Nelson,W., DeBoy,R., Kolonay,J., McClarty,G., Salzberg,S.L., Eisen,J. and Fraser,C.M.
Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39 Nucleic Acids Res 2000 Mar 15;28(6):1397-406
Chlamydophila caviae GPIC
Read,T.D., Myers,G.S., Brunham,R.C., Nelson,W.C., Paulsen,I.T., Heidelberg,J., Holtzapple,E., Khouri,H., Federova,N.B., Carty,H.A., Umayam,L.A., Haft,D.H., Peterson,J., Beanan,M.J., White,O., Salzberg,S.L., Hsia,R.C., McClarty,G., Rank,R.G., Bavoil,P.M. and Fraser,C.M.
Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae Nucleic Acids Res. 31 (8), 2134-2147 (2003)
Chlamydophila pneumoniae
Kalman,S., Mitchell,W., Marathe,R., Lammel,C., Fan,J., Hyman,R.W., Olinger,L., Grimwood,J., Davis,R.W. and Stephens,R.S.
Comparative genomes of Chlamydia pneumoniae and C. trachomatis Nat Genet 1999 Apr;21(4):385-9
Chlamydophila pneumoniae J138
Shirai,M., Hirakawa,H., Kimoto,M., Tabuchi,M., Kishi,F., Ouchi,K., Shiba,T., Ishii,K., Hattori,M., Kuhara,S. and Nakazawa,T.
Comparison of whole genome sequences of Chlamydia pneumoniae J138 from Japan and CWL029 from USA Nucleic Acids Res 2000 Jun 15;28(12):2311-4
Chlamydophila pneumoniae TW-183
Geng,M.M., Schuhmacher,A., Muehldorfer,I., Bensch,K.W.,Schaefer,K.P., Schneider,S., Pohl,T., Essig,A., Marre,R. and Melchers,K.
The genome sequence of Chlamydia pneumoniae TW183 and comparison with other Chlamydia strains based on whole genome sequence analysis
Unpublished
Chlorobium tepidum TLS
Eisen,J.A., Nelson,K.E., Paulsen,I.T., Heidelberg,J.F., Wu,M., Dodson,R.J., Deboy,R., Gwinn,M.L., Nelson,W.C., Haft,D.H., Hickey,E.K., Peterson,J.D., Durkin,A.S., Kolonay,J.L., Yang,F., Holt,I., Umayam,L.A., Mason,T., Brenner,M., Shea,T.P., Parksey,D., Nierman,W.C., Feldblyum,T.V., Hansen,C.L., Craven,M.B., Radune,D., Vamathevan,J., Khouri,H., White,O., Gruber,T.M., Ketchum,K.A., Venter,J.C., Tettelin,,H., Bryant,D.A. and Fraser,C.M.
The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium Proc Natl Acad Sci U S A. 2002 Jul 9;99(14):9509-14. Epub 2002 Jul 01.
Dehalococcoides ethenogenes 195
Seshadri R, Adrian L, Fouts DE, Eisen JA, Phillippy AM, Methe BA, Ward NL, Nelson WC, Deboy RT, Khouri HM, Kolonay JF, Dodson RJ, Daugherty SC, Brinkac LM, Sullivan SA, Madupu R, Nelson KE, Kang KH, Impraim M, Tran K, Robinson JM, Forberger HA, Fraser CM, Zinder SH, Heidelberg JF.
Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes. Science. 2005 Jan 7;307(5706):105-8.
Gloeobacter violaceus PCC 7421
Nakamura Y, Kaneko T, Sato S, Mimuro M, Miyashita H, Tsuchiya T, Sasamoto S, Watanabe A, Kawashima K, Kishida Y, Kiyokawa C, Kohara M, Matsumoto M, Matsuno A, Nakazaki N, Shimpo S, Takeuchi C, Yamada M, Tabata S.
Complete genome structure of Gloeobacter violaceus PCC 7421, a cyanobacterium that lacks thylakoids. DNA Res. 2003 Aug 31;10(4):137-45.
Synechocystis PCC6803
Kaneko T, Sato S, Kotani H, Tanaka A, Asamizu E, Nakamura Y, Miyajima N, Hirosawa M, Sugiura M, Sasamoto S, Kimura T, Hosouchi T, Matsuno A, Muraki A, Nakazaki N, Naruo K, Okumura S, Shimpo S, Takeuchi C, Wada T, Watanabe A, Yamada M, Yasuda M, Tabata S.
Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res 1996 Jun 30;3(3):109-36
Thermosynechococcus elongatus BP-1
kamura,Y., Kaneko,T., Sato,S., Ikeuchi,M., Katoh,H., Sasamoto,S., Watanabe,A., Iriguchi,M., Kawashima,K., Kimura,T., Kishida,Y., Kiyokawa,C., Kohara,M., Matsumoto,M., Matsuno,A., Nakazaki,N., Shimpo,S., Sugimoto,M., Takeuchi,C., Yamada,M. and Tabata,S.
Complete genome structure of the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 DNA Res. 2002 Aug 31;9(4):123-30.
Anabaena sp. strain PCC 7120
Kaneko T, Nakamura Y, Wolk CP, Kuritz T, Sasamoto S, Watanabe A, Iriguchi M, Ishikawa A, Kawashima K, Kimura T, Kishida Y, Kohara M, Matsumoto M, Matsuno A, Muraki A, Nakazaki N, Shimpo S, Sugimoto M, Takazawa M, Yamada M, Yasuda M, Tabata S.
Complete genomic sequence of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120. DNA Res. 8 (5), 205-213 (2001)
Prochlorococcus marinus MED4
Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, Ahlgren NA, Arellano A, Coleman M, Hauser L, Hess WR, Johnson ZI, Land M, Lindell D, Post AF, Regala W, Shah M, Shaw SL, Steglich C, Sullivan MB, Ting CS, Tolonen A, Webb EA, Zinser ER, Chisholm SW.
Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature. 2003 Aug 28;424(6952):1042-7. Epub 2003 Aug 13.
Prochlorococcus marinus MIT9313
Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, Ahlgren NA, Arellano A, Coleman M, Hauser L, Hess WR, Johnson ZI, Land M, Lindell D, Post AF, Regala W, Shah M, Shaw SL, Steglich C, Sullivan MB, Ting CS, Tolonen A, Webb EA, Zinser ER, Chisholm SW.
Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature. 2003 Aug 28;424(6952):1042-7. Epub 2003 Aug 13.
Prochlorococcus marinus marinus CCMP1375
Dufresne A, Salanoubat M, Partensky F, Artiguenave F, Axmann IM, Barbe V, Duprat S, Galperin MY, Koonin EV, Le Gall F, Makarova KS, Ostrowski M, Oztas S, Robert C, Rogozin IB, Scanlan DJ, Tandeau de Marsac N, Weissenbach J, Wincker P, Wolf YI, Hess WR.
Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome. Proc Natl Acad Sci U S A. 2003 Aug 19;100(17):10020-5. Epub 2003 Aug 13.
Bacillus halodurans C-125
Takami,H., Nakasone,K., Hirama,C., Takaki,Y., Masui,N., Fuji,F., Nakamura,Y. and Inoue,A.
An improved physical and genetic map of the genome of alkaliphilic Bacillus sp. C-125 Extremophiles 1999 Jan;3(1):21-8
Bacillus licheniformis DSM 13
Veith B, Herzberg C, Steckel S, Feesche J, Maurer KH, Ehrenreich P, Baumer S, Henne A, Liesegang H, Merkl R, Ehrenreich A, Gottschalk G.
The complete genome sequence of Bacillus licheniformis DSM13, an organism with great industrial potential. J Mol Microbiol Biotechnol. 2004;7(4):204-11.
Bacillus licheniformis ATCC 14580
Rey MW, Ramaiya P, Nelson BA, Brody-Karpin SD, Zaretsky EJ, Tang M, Lopez de Leon A, Xiang H, Gusti V, Clausen IG, Olsen PB, Rasmussen MD, Andersen JT, Jorgensen PL, Larsen TS, Sorokin A, Bolotin A, Lapidus A, Galleron N, Ehrlich SD, Berka RM.
Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species. Genome Biol. 2004;5(10):R77. Epub 2004 Sep 13.
Bacillus anthracisstr. Ames 0581
Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, Tettelin H, Fouts DE, Eisen JA, Gill SR, Holtzapple EK, Okstad OA, Helgason E, Rilstone J, Wu M, Kolonay JF, Beanan MJ, Dodson RJ, Brinkac LM, Gwinn M, DeBoy RT, Madpu R, Daugherty SC, Durkin AS, Haft DH, Nelson WC, Peterson JD, Pop M, Khouri HM, Radune D, Benton JL, Mahamoud Y, Jiang L, Hance IR, Weidman JF, Berry KJ, Plaut RD, Wolf AM, Watkins KL, Nierman WC, Hazen A, Cline R, Redmond C, Thwaite JE, White O, Salzberg SL, Thomason B, Friedlander AM, Koehler TM, Hanna PC, Kolsto AB, Fraser CM.
The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature. 2003 May 1;423(6935):81-6.
Bacillus anthracis str. Sterne
Brettin,T.S., Bruce,D., Challacombe,J.F., Gilna,P., Han,C.,Hill,K., Hitchcock,P., Jackson,P., Keim, P., Longmire,J., Lucas,S.,Okinaka,R., Richardson,P., Rubin,E. and Tice,H.
Complete genome sequence of Bacillus anthracis Sterne Unpublished
Bacillus cereus ATCC 10987
Rasko DA, Ravel J, Okstad OA, Helgason E, Cer RZ, Jiang L, Shores KA, Fouts DE, Tourasse NJ, Angiuoli SV, Kolonay J, Nelson WC, Kolsto AB, Fraser CM, Read TD.
The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1. Nucleic Acids Res. 2004 Feb 11;32(3):977-88. Print 2004.
Listeria innocua Clip11262 Listeria monocytogenes EGD-e
Glaser P, Frangeul L, Buchrieser C, Rusniok C, Amend A, Baquero F, Berche P, Bloecker H, Brandt P, Chakraborty T, Charbit A, Chetouani F, Couve E, de Daruvar A, Dehoux P, Domann E, Dominguez-Bernal G, Duchaud E, Durant L, Dussurget O, Entian KD, Fsihi H, Portillo FG, Garrido P, Gautier L, Goebel W, Gomez-Lopez N, Hain T, Hauf J, Jackson D, Jones LM, Kaerst U, Kreft J, Kuhn M, Kunst F, Kurapkat G, Madueno E, Maitournam A, Vicente JM, Ng E, Nedjari H, Nordsiek G, Novella S, de Pablos B, Perez-Diaz JC, Purcell R, Remmel B, Rose M, Schlueter T, Simoes N, Tierrez A, Vazquez-Boland JA, Voss H, Wehland J, Cossart P.
Comparative genomics of Listeria species. Science 2001 Oct 26;294(5543):849-52
Listeria monocytogenes str. 4b F2365
Nelson KE, Fouts DE, Mongodin EF, Ravel J, DeBoy RT, Kolonay JF, Rasko DA, Angiuoli SV, Gill SR, Paulsen IT, Peterson J, White O, Nelson WC, Nierman W, Beanan MJ, Brinkac LM, Daugherty SC, Dodson RJ, Durkin AS, Madupu R, Haft DH, Selengut J, Van Aken S, Khouri H, Fedorova N, Forberger H, Tran B, Kathariou S, Wonderling LD, Uhlich GA, Bayles DO, Luchansky JB, Fraser CM.
Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species. Nucleic Acids Res. 2004 Apr 28;32(8):2386-95. Print 2004.
Staphylococcus aureus Mu50
Kuroda M, Ohta T, Uchiyama I, Baba T, Yuzawa H, Kobayashi I, Cui L, Oguchi A, Aoki K, Nagai Y, Lian J, Ito T, Kanamori M, Matsumaru H, Maruyama A, Murakami H, Hosoyama A, Mizutani-Ui Y, Takahashi NK, Sawano T, Inoue R, Kaito C, Sekimizu K, Hirakawa H, Kuhara S, Goto S, Yabuzaki J, Kanehisa M, Yamashita A, Oshima K, Furuya K, Yoshino C, Shiba T, Hattori M, Ogasawara N, Hayashi H, Hiramatsu K.
Whole genome sequencing of meticillin-resistant Staphylococcus aureus. Lancet. 2001 Apr 21;357(9264):1225-40.
Staphylococcus aureus MW2
Baba,T., Takeuchi,F., Kuroda,M., Yuzawa,H., Aoki,K., Oguchi,A., Nagai,Y., Iwama,N., Asano,K., Naimi,T., Kuroda,H., Cui,L., Yamamoto,K. and Hiramatsu,K.
Genome and virulence determinants of high virulence community-acquired MRSA ancet 359 (9320), 1819-1827 (2002)
Staphylococcus aureus subsp. aureus COL
Gill SR, Fouts DE, Archer GL, Mongodin EF, Deboy RT, Ravel J, Paulsen IT, Kolonay JF, Brinkac L, Beanan M, Dodson RJ, Daugherty SC, Madupu R, Angiuoli SV, Durkin AS, Haft DH, Vamathevan J, Khouri H, Utterback T, Lee C, Dimitrov G, Jiang L, Qin H, Weidman J, Tran K, Kang K, Hance IR, Nelson KE, Fraser CM.
Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain. J Bacteriol. 2005 Apr;187(7):2426-38.
Staphylococcus epidermidis ATCC 12228
Zhang YQ, Ren SX, Li HL, Wang YX, Fu G, Yang J, Qin ZQ, Miao YG, Wang WY, Chen RS, Shen Y, Chen Z, Yuan ZH, Zhao GP, Qu D, Danchin A, Wen YM.
Genome-based analysis of virulence genes in a non-biofilm-forming Staphylococcus epidermidis strain (ATCC 12228). Mol Microbiol. 2003 Sep;49(6):1577-93.
Staphylococcus epidermidis RP62A
Gill SR, Fouts DE, Archer GL, Mongodin EF, Deboy RT, Ravel J, Paulsen IT, Kolonay JF, Brinkac L, Beanan M, Dodson RJ, Daugherty SC, Madupu R, Angiuoli SV, Durkin AS, Haft DH, Vamathevan J, Khouri H, Utterback T, Lee C, Dimitrov G, Jiang L, Qin H, Weidman J, Tran K, Kang K, Hance IR, Nelson KE, Fraser CM.
Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain. J Bacteriol. 2005 Apr;187(7):2426-38.
Staphylococcus aureus subsp. aureus MRSA252
Holden MT, Feil EJ, Lindsay JA, Peacock SJ, Day NP, Enright MC, Foster TJ, Moore CE, Hurst L, Atkin R, Barron A, Bason N, Bentley SD, Chillingworth C, Chillingworth T, Churcher C, Clark L, Corton C, Cronin A, Doggett J, Dowd L, Feltwell T, Hance Z, Harris B, Hauser H, Holroyd S, Jagels K, James KD, Lennard N, Line A, Mayes R, Moule S, Mungall K, Ormond D, Quail MA, Rabbinowitsch E, Rutherford K, Sanders M, Sharp S, Simmonds M, Stevens K, Whitehead S, Barrell BG, Spratt BG, Parkhill J.
Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance. Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9786-91. Epub 2004 Jun 22.
Staphylococcus aureus subsp. aureus MSSA476
Holden MT, Feil EJ, Lindsay JA, Peacock SJ, Day NP, Enright MC, Foster TJ, Moore CE, Hurst L, Atkin R, Barron A, Bason N, Bentley SD, Chillingworth C, Chillingworth T, Churcher C, Clark L, Corton C, Cronin A, Doggett J, Dowd L, Feltwell T, Hance Z, Harris B, Hauser H, Holroyd S, Jagels K, James KD, Lennard N, Line A, Mayes R, Moule S, Mungall K, Ormond D, Quail MA, Rabbinowitsch E, Rutherford K, Sanders M, Sharp S, Simmonds M, Stevens K, Whitehead S, Barrell BG, Spratt BG, Parkhill J.
Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance. Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9786-91. Epub 2004 Jun 22.
Clostridium acetobutylicum
Nolling,J., Breton,G., Omelchenko,M.V., Markarova,K.S., Zeng,Q., Gibson,R., Lee,H.M., Dubois,J., Qiu,D., Hitti,J., Wolf,Y.I., Tatusov,R.L., Sabathe,F., Doucette-Stamm,L., Soucaille,P., Daly,M.J., Bennett,G.N., Koonin,E.V. and Smith,D.R.
Genome Sequence and Comparative Analysis of the Solvent-Producing Bacterium Clostridium acetobutylicum J Bacteriol 2001 Aug;183(16):4823-38
Lactobacillus johnsonii NCC 533
Pridmore RD, Berger B, Desiere F, Vilanova D, Barretto C, Pittet AC, Zwahlen MC, Rouvet M, Altermann E, Barrangou R, Mollet B, Mercenier A, Klaenhammer T, Arigoni F, Schell MA.
The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533. Proc Natl Acad Sci U S A. 2004 Feb 24;101(8):2512-7.
Lactobacillus plantarum WCFS1
Kleerebezem,M., Boekhorst,J., van Kranenburg,R., Molenaar,D., Kuipers,O.P., Leer,R., Tarchini,R., Peters,S.A., Sandbrink,H.M., Fiers,M.W.E.J., Stiekema,W., Klein Lankhorst,R.M., Bron,P.A., Hoffer,S.M., Nierop Groot,M.N., Kerkhoven,R., de Vries,M., Ursing,B., de Vos,W.M. and Siezen,R.J.
Complete genome sequence of Lactobacillus plantarum WCFS1 Proc Natl Acad Sci U S A. 2003 Feb 18;100(4):1990-5. Epub 2003 Feb 03.
Lactococcus lactis subsp. lactis
Bolotin,A., Wincker,P., Mauger,S., Jaillon,O., Malarme,K., Weissenbach,J., Ehrlich,S.D. and Sorokin,A.
The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403. Genome Res 2001 May;11(5):731-53
Streptococcus agalactiae 2603V/R
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Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae Proc Natl Acad Sci U S A. 2002 Sep 17;99(19):12391-6. Epub 2002 Aug 28.
Streptococcus pyogenes
Ferretti,J.J., McShan,W.M., Adjic,D., Savic,D., Savic,G., Lyon,K., Primeaux,C., Sezate,S.S., Surorov,A.N., Kenton,S., Lai,H., Lin,S., Qian,Y., Jia,H.G., Najar,F.Z., Ren,Q., Zhu,H., Song,L., White,J., Yuan,X., Clifton,S.W., Roe,B.A. and McLaughlin,R.E.
Complete genome sequence of an M1 strain of Streptococcus pyogenes Proc Natl Acad Sci U S A 2001 Apr 10;98(8):4658-63
Streptococcus pyogenes strain MGAS8232
Smoot,J.C., Barbian,K.D., Van Gompel,J.J., Smoot,L.M., Chaussee,M.S., Sylva,G.L., Sturdevant,D.E., Ricklefs,S.M., Porcella,S.F., Parkins,L.D., Beres,S.B., Campbell,D.S., Smith,T.M., Zhang,Q., Kapur,V., Daly,J.A., Veasy,L.G. and Musser,J.M.
Genome sequence and comparative microarray analysis of serotype M18 group A Streptococcus strains associated with acute rheumatic fever outbreaks Proc. Natl. Acad. Sci. U.S.A. 99 (7), 4668-4673 (2002)
Streptococcus pyogenes MGAS315
Beres,S.B., Sylva,G.L., Barbian,K.D., Lei,B., Hoff,J.S., Mammarella,N.D., Liu,M.-Y., Smoot,J.C., Porcella,S.F., Parkins,L.D., McCormick,J.K., Leung,D.Y.M., Schlievert,P.M. and Musser,J.M.
Genome sequence of a serotype M3 strain of group A Streptococcus: phage-encoded toxins, the high-virulence phenotype, and clone emergence Proc. Natl. Acad. Sci. U.S.A. 99 (15), 10078-10083 (2002)
Streptococcus pyogenes SSI-1
Nakagawa I, Kurokawa K, Yamashita A, Nakata M, Tomiyasu Y, Okahashi N, Kawabata S, Yamazaki K, Shiba T, Yasunaga T, Hayashi H, Hattori M, Hamada S.
Genome sequence of an M3 strain of Streptococcus pyogenes reveals a large-scale genomic rearrangement in invasive strains and new insights into phage evolution. Genome Res. 2003 Jun;13(6A):1042-55.
Streptococcus thermophilus CNRZ1066
Bolotin A, Quinquis B, Renault P, Sorokin A, Ehrlich SD, Kulakauskas S, Lapidus A, Goltsman E, Mazur M, Pusch GD, Fonstein M, Overbeek R, Kyprides N, Purnelle B, Prozzi D, Ngui K, Masuy D, Hancy F, Burteau S, Boutry M, Delcour J, Goffeau A, Hols P.
Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus. Nat Biotechnol. 2004 Dec;22(12):1554-8. Epub 2004 Nov 14.
Streptococcus thermophilus LMG 18311
Bolotin A, Quinquis B, Renault P, Sorokin A, Ehrlich SD, Kulakauskas S, Lapidus A, Goltsman E, Mazur M, Pusch GD, Fonstein M, Overbeek R, Kyprides N, Purnelle B, Prozzi D, Ngui K, Masuy D, Hancy F, Burteau S, Boutry M, Delcour J, Goffeau A, Hols P.
Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus. Nat Biotechnol. 2004 Dec;22(12):1554-8. Epub 2004 Nov 14.
Mycoplasma pulmonis
Chambaud,I., Heilig,R., Ferris,S., Barbe,V., Samson,D., Galisson,F., Moszer,I., Dybvig,K., Wroblewski,H., Viari,A., Rocha,E.P.C. and Blanchard,A.
The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis Nucleic Acids Res 2001 May 15;29(10):2145-53
Mycoplasma mycoides subsp. mycoides SC
Westberg J, Persson A, Holmberg A, Goesmann A, Lundeberg J, Johansson KE, Pettersson B, Uhlen M.
The genome sequence of Mycoplasma mycoides subsp. mycoides SC type strain PG1T, the causative agent of contagious bovine pleuropneumonia (CBPP). Genome Res. 2004 Feb;14(2):221-7.
Rhodopseudomonas palustris
Larimer FW, Chain P, Hauser L, Lamerdin J, Malfatti S, Do L, Land ML, Pelletier DA, Beatty JT, Lang AS, Tabita FR, Gibson JL, Hanson TE, Bobst C, Torres JL, Peres C, Harrison FH, Gibson J, Harwood CS.
Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris. Nat Biotechnol. 2004 Jan;22(1):55-61. Epub 2003 Dec 14.
Brucella melitensis 16M
DelVecchio,V.G., Kapatral,V., Redkar,R.J., Patra,G., Mujer,C., Los,T., Ivanova,N., Anderson,I., Bhattacharyya,A., Lykidis,A., Reznik,G., Jablonski,L., Larsen,N., D'Souza,M., Bernal,A., Mazur,M., Goltsman,E., Selkov,E., Elzer,P.H., Hagius,S., O'Callaghan,D., Letesson,J.-J., Haselkorn,R., Kyrpides,N. and Overbeek,R.
The genome sequence of the facultative intracellular pathogen Brucella melitensis Proc. Natl. Acad. Sci. U.S.A. 99 (1), 443-448 (2002)
Brucella suis 1330
Paulsen IT, Seshadri R, Nelson KE, Eisen JA, Heidelberg JF, Read TD, Dodson RJ, Umayam L, Brinkac LM, Beanan MJ, Daugherty SC, Deboy RT, Durkin AS, Kolonay JF, Madupu R, Nelson WC, Ayodeji B, Kraul M, Shetty J, Malek J, Van Aken SE, Riedmuller S, Tettelin H, Gill SR, White O, Salzberg SL, Hoover DL, Lindler LE, Halling SM, Boyle SM, Fraser CM.
The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc Natl Acad Sci U S A. 2002 Oct 1;99(20):12503-5.
Sinorhizobium meliloti 1021
Barnett,M.J., Fisher,R.F., Jones,T., Komp,C., Abola,A.P., Barloy-Hubler,F., Bowser,L., Capela,D., Galibert,F., Gouzy,J., Gurjal,M., Hong,A., Huizar,L., Hyman,R.W., Kahn,D., Kahn,M.L., Kalman,S., Keating,D.H., Palm,C., Peck,M.C., Surzycki,R., Wells,D.H., Yeh,K.-C., Davis,R.W., Federspiel,N.A. and Long,S.R.
Nucleotide Sequence and Predicted Functions of the Entire Sinorhizobium meliloti pSymA Megaplasmid Proc Natl Acad Sci U S A 2001 Aug 14;98(17):9883-8
Silicibacter pomeroyi DSS-3
Moran MA, Buchan A, Gonzalez JM, Heidelberg JF, Whitman WB, Kiene RP, Henriksen JR, King GM, Belas R, Fuqua C, Brinkac L, Lewis M, Johri S, Weaver B, Pai G, Eisen JA, Rahe E, Sheldon WM, Ye W, Miller TR, Carlton J, Rasko DA, Paulsen IT, Ren Q, Daugherty SC, Deboy RT, Dodson RJ, Durkin AS, Madupu R, Nelson WC, Sullivan SA, Rosovitz MJ, Haft DH, Selengut J, Ward N.
Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature. 2004 Dec 16;432(7019):910-3.
Ehrlichia ruminantium Welgevonden(ARC-OVI)
Collins NE, Liebenberg J, de Villiers EP, Brayton KA, Louw E, Pretorius A, Faber FE, van Heerden H, Josemans A, van Kleef M, Steyn HC, van Strijp MF, Zweygarth E, Jongejan F, Maillard JC, Berthier D, Botha M, Joubert F, Corton CH, Thomson NR, Allsopp MT, Allsopp BA.
The genome of the heartwater agent Ehrlichia ruminantium contains multiple tandem repeats of actively variable copy number. Proc Natl Acad Sci U S A. 2005 Jan 18;102(3):838-43. Epub 2005 Jan 6.
Ehrlichia ruminantium str. Welgevonden(CIRAD)
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Unpublished
Ehrlichia ruminantium str. Gardel
Frutos,R., Ferraz,C., Bensaid,A., Eychenie,S., Kandassami,Y., Chantal,I., Morgat,A., Coissac,E., Vachiery,N., Demaille,J., Viari,A. and Martinez,D.
Unpublished
Rickettsia prowazekii Madrid E
Andersson,S.G., Zomorodipour,A., Andersson,J.O., Sicheritz-Ponten,T., Alsmark,U.C., Podowski,R.M., Naslund,A.K., Eriksson,A.S., Winkler,H.H. and Kurland,C.G.
Thegenome sequence of Rickettsia prowazekii and the origin of mitochondria Nature 1998 Nov 12;396(6707):133-40
Rickettsia typhi str. Wilmington
McLeod MP, Qin X, Karpathy SE, Gioia J, Highlander SK, Fox GE, McNeill TZ, Jiang H, Muzny D, Jacob LS, Hawes AC, Sodergren E, Gill R, Hume J, Morgan M, Fan G, Amin AG, Gibbs RA, Hong C, Yu XJ, Walker DH, Weinstock GM.
Complete genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae. J Bacteriol. 2004 Sep;186(17):5842-55.
Wolbachia endosymbiont of Drosophila melanogaster
Wu M, Sun LV, Vamathevan J, Riegler M, Deboy R, Brownlie JC, McGraw EA, Martin W, Esser C, Ahmadinejad N, Wiegand C, Madupu R, Beanan MJ, Brinkac LM, Daugherty SC, Durkin AS, Kolonay JF, Nelson WC, Mohamoud Y, Lee P, Berry K, Young MB, Utterback T, Weidman J, Nierman WC, Paulsen IT, Nelson KE, Tettelin H, O'Neill SL, Eisen JA.
Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. PLoS Biol. 2004 Mar;2(3):E69. Epub 2004 Mar 16.
Wolbachia endosymbiont strain TRS of Brugia malayi
Foster J, Ganatra M, Kamal I, Ware J, Makarova K, Ivanova N, Bhattacharyya A, Kapatral V, Kumar S, Posfai J, Vincze T, Ingram J, Moran L, Lapidus A, Omelchenko M, Kyrpides N, Ghedin E, Wang S, Goltsman E, Joukov V, Ostrovskaya O, Tsukerman K, Mazur M, Comb D, Koonin E, Slatko B.
The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode. PLoS Biol. 2005 Apr;3(4):e121. Epub 2005 Mar 29.
Bdellovibrio bacteriovorus HD100
Rendulic S, Jagtap P, Rosinus A, Eppinger M, Baar C, Lanz C, Keller H, Lambert C, Evans KJ, Goesmann A, Meyer F, Sockett RE, Schuster SC.
A predator unmasked: life cycle of Bdellovibrio bacteriovorus from a genomic perspective. Science. 2004 Jan 30;303(5658):689-92.
Desulfotalea psychrophila LSv54
Rabus R, Ruepp A, Frickey T, Rattei T, Fartmann B, Stark M, Bauer M, Zibat A, Lombardot T, Becker I, Amann J, Gellner K, Teeling H, Leuschner WD, Glockner FO, Lupas AN, Amann R, Klenk HP.
The genome of Desulfotalea psychrophila, a sulfate-reducing bacterium from permanently cold Arctic sediments. Environ Microbiol. 2004 Sep;6(9):887-902.
Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough
Heidelberg JF, Seshadri R, Haveman SA, Hemme CL, Paulsen IT, Kolonay JF, Eisen JA, Ward N, Methe B, Brinkac LM, Daugherty SC, Deboy RT, Dodson RJ, Durkin AS, Madupu R, Nelson WC, Sullivan SA, Fouts D, Haft DH, Selengut J, Peterson JD, Davidsen TM, Zafar N, Zhou L, Radune D, Dimitrov G, Hance M, Tran K, Khouri H, Gill J, Utterback TR, Feldblyum TV, Wall JD, Voordouw G, Fraser CM.
The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Nat Biotechnol. 2004 May;22(5):554-9. Epub 2004 Apr 11.
Geobacter sulfurreducens PCA
Methe BA, Nelson KE, Eisen JA, Paulsen IT, Nelson W, Heidelberg JF, Wu D, Wu M, Ward N, Beanan MJ, Dodson RJ, Madupu R, Brinkac LM, Daugherty SC, DeBoy RT, Durkin AS, Gwinn M, Kolonay JF, Sullivan SA, Haft DH, Selengut J, Davidsen TM, Zafar N, White O, Tran B, Romero C, Forberger HA, Weidman J, Khouri H, Feldblyum TV, Utterback TR, Van Aken SE, Lovley DR, Fraser CM.
Genome of Geobacter sulfurreducens: metal reduction in subsurface environments. Science. 2003 Dec 12;302(5652):1967-9.
Campylobacter jejuni RM1221
Fouts DE, Mongodin EF, Mandrell RE, Miller WG, Rasko DA, Ravel J, Brinkac LM, DeBoy RT, Parker CT, Daugherty SC, Dodson RJ, Durkin AS, Madupu R, Sullivan SA, Shetty JU, Ayodeji MA, Shvartsbeyn A, Schatz MC, Badger JH, Fraser CM, Nelson KE.
Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species. PLoS Biol. 2005 Jan;3(1):e15. Epub 2005 Jan 4.
Helicobacter hepaticus ATCC 51449
Suerbaum S, Josenhans C, Sterzenbach T, Drescher B, Brandt P, Bell M, Droge M, Fartmann B, Fischer HP, Ge Z, Horster A, Holland R, Klein K, Konig J, Macko L, Mendz GL, Nyakatura G, Schauer DB, Shen Z, Weber J, Frosch M, Fox JG.
The complete genome sequence of the carcinogenic bacterium Helicobacter hepaticus. Proc Natl Acad Sci U S A. 2003 Jun 24;100(13):7901-6. Epub 2003 Jun 16.
Idiomarina loihiensis L2TR
Hou S, Saw JH, Lee KS, Freitas TA, Belisle C, Kawarabayasi Y, Donachie SP, Pikina A, Galperin MY, Koonin EV, Makarova KS, Omelchenko MV, Sorokin A, Wolf YI, Li QX, Keum YS, Campbell S, Denery J, Aizawa S, Shibata S, Malahoff A, Alam M.
Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy. Proc Natl Acad Sci U S A. 2004 Dec 28;101(52):18036-41. Epub 2004 Dec 13.
Buchnera aphidicola
Tamas,I., Klasson,L., Canback,B., Naslund,A.K., Eriksson,A.S., Wernegreen,J.J., Sandstrom,J.P., Moran,N.A. and Andersson,S.G.
50 million years of genomic stasis in endosymbiotic bacteria Science 296 (5577), 2376-2379 (2002)
Buchnera sp. APS
Shigenobu,S., Watanabe,H., Hattori,M., Sakaki,Y. and Ishikawa,H.
Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS Nature 2000 Sep 7;407(6800):81-6
Escherichia coli K-12 MG1655
Blattner,F.R., Plunkett,G. III, Bloch,C.A., Perna,N.T., Burland,V., Riley,M., Collado-Vides,J., Glasner,J.D., Rode,C.K., Mayhew,G.F., Gregor,J., Davis,N.W., Kirkpatrick,H.A., Goeden,M.A., Rose,D.J., Mau,B. and Shao,Y.
The complete genome sequence of Escherichia coli K-12 Science 1997 Sep 5;277(5331):1453-74
Escherichia coli O157:H7
Makino,K., Yokoyama,K., Kubota,Y., Yutsudo,C.H., Kimura,S., Kurokawa,K., Ishii,K., Hattori,M., Tatsuno,I., Abe,H., Iida,T., Yamamoto,K., Ohnishi,M., Hayashi,T., Yasunaga,T., Honda,T., Sasakawa,C. and Shinagawa,H.
Complete nucleotide sequence of the prophage VT2-Sakai carrying the verotoxin 2 genes of the enterohemorrhagic Escherichia coli O157:H7 derived from the Sakai outbreak DNA Res 2001 Feb 28;8(1):11-22
Escherichia coli CFT073
Welch RA, Burland V, Plunkett G 3rd, Redford P, Roesch P, Rasko D, Buckles EL, Liou SR, Boutin A, Hackett J, Stroud D, Mayhew GF, Rose DJ, Zhou S, Schwartz DC, Perna NT, Mobley HL, Donnenberg MS, Blattner FR.
Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc Natl Acad Sci U S A 2002 Dec 24;99(26):17020-4
Erwinia carotovora subsp. atroseptica SCRI1043
Bell KS, Sebaihia M, Pritchard L, Holden MT, Hyman LJ, Holeva MC, Thomson NR, Bentley SD, Churcher LJ, Mungall K, Atkin R, Bason N, Brooks K, Chillingworth T, Clark K, Doggett J, Fraser A, Hance Z, Hauser H, Jagels K, Moule S, Norbertczak H, Ormond D, Price C, Quail MA, Sanders M, Walker D, Whitehead S, Salmond GP, Birch PR, Parkhill J, Toth IK.
Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors. Proc Natl Acad Sci U S A. 2004 Jul 27;101(30):11105-10. Epub 2004 Jul 19
Photorhabdus luminescens laumondii TTO1
Duchaud E, Rusniok C, Frangeul L, Buchrieser C, Givaudan A, Taourit S, Bocs S, Boursaux-Eude C, Chandler M, Charles JF, Dassa E, Derose R, Derzelle S, Freyssinet G, Gaudriault S, Medigue C, Lanois A, Powell K, Siguier P, Vincent R, Wingate V, Zouine M, Glaser P, Boemare N, Danchin A, Kunst F.
The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens. Nat Biotechnol. 2003 Nov;21(11):1307-13. Epub 2003 Oct 05.
Salmonella typhi CT18 Salmonella typhimurium LT2
McClelland M, Sanderson KE, Spieth J, Clifton SW, Latreille P, Courtney L, Porwollik S, Ali J, Dante M, Du F, Hou S, Layman D, Leonard S, Nguyen C, Scott K, Holmes A, Grewal N, Mulvaney E, Ryan E, Sun H, Florea L, Miller W, Stoneking T, Nhan M, Waterston R, Wilson RK.
Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature 2001 Oct 25;413(6858):852-6
Salmonella enterica subsp. enterica serovar Paratypi A str. ATCC 9150
McClelland M, Sanderson KE, Clifton SW, Latreille P, Porwollik S, Sabo A, Meyer R, Bieri T, Ozersky P, McLellan M, Harkins CR, Wang C, Nguyen C, Berghoff A, Elliott G, Kohlberg S, Strong C, Du F, Carter J, Kremizki C, Layman D, Leonard S, Sun H, Fulton L, Nash W, Miner T, Minx P, Delehaunty K, Fronick C, Magrini V, Nhan M, Warren W, Florea L, Spieth J, Wilson RK.
Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid. Nat Genet. 2004 Dec;36(12):1268-74. Epub 2004 Nov 7.
Shigella flexneri 2a 301
Jin,Q., Yuan,Z.H., Xu,J.G., Wang,Y., Shen,Y., Lu,W.C., Wang,J.H., Liu,H., Yang,J., Yang,F., Qu,D., Zhang,X.B., Zhang,J.Y., Yang,G.W., Wu,H.T., Dong,J., Sun,L.L., Xue,Y., Zhao,A.L., Gao,Y.S., Zhu,J.P., Kan,B., Chen,S.X., Yao,Z.J., He,B.K., Chen,R.S., Ma,D.L., Qiang,B.Q., Wen,Y.M., Hou,Y.D. and Yu,J.
Genome Sequence of Shigella flexneri 2a, Insights into Pathogenicity through Comparison with Genomes of Escherichia coli K12 and O157 Nucleic Acids Res. 2002 Oct 15;30(20):4432-41.
Shigella flexneri 2a str. 2457T
Wei,J., Goldberg,M.B., Burland,V., Venkatesan,M.M., Deng,W., Fournier,G., Mayhew,G.F., Plunkett,G. III, Rose,D.J., Darling,A., Mau,B., Perna,N.T., Payne,S.M., Runyen-Janecky,L.J., Zhou,S., Schwartz,D.C. and Blattner,F.R.
Complete Genome Sequence and Comparative Genomics of Shigella flexneri Serotype 2a Strain 2457T Infect Immun. 2003 May;71(5):2775-86.
Wigglesworthia brevipalpis
Akman,L., Yamashita,A., Watanabe,H., Oshima,K., Shiba,T., Hattori,M. and Aksoy,S.
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Yersinia pestis CO92
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Yersinia pestis biovar Mediaevails str. 91001
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Direct Submission
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Coxiella burnetii RSA 493
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Legionella pneumophila subsp. pneumophila str. Philadelphia 1
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Methylococcus capsulatus str. Bath
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Haemophilus ducreyi 35000HP
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Xylella fastidiosa 9a5c
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Xylella fastidiosa Temecula1
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Leptospira interrogans serovar lai
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Unpublished Chinese National Human Genome Center at Shanghai, 250 Bi Bo Road, Shanghai, Shanghai 201203, China
Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130
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Treponema denticola ATCC 35405
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Thermotoga maritima MSB8
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Cryptosporidium hominis
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Genome Sequneces(Eukaryota)
Plasmodium falciparum
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Plasmodium yoelii yoelii
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Thalassiosira pseudonana CCMP1335
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Maheswari U, Montsant A, Goll J, Krishnasamy S, Rajyashri KR, Patell VM, Bowler C.
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Neurospora crassa
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Yarrowia lipolytica CLIB99 Debaryomyces hansenii CBS767 Kluyveromyces lactis NRRL Y-1140
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Naumovia castellii
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Candida glabrata CBS138
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Ashbya gossypii
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Drosophila melanogaster
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Bombyx mori
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Anopheles gambiae
The Anopheles Genome Sequencing Consortium
Direct Submission
Takifugu rubripes rubripes
Elgar G, Clark MS, Meek S, Smith S, Warner S, Edwards YJ, Bouchireb N, Cottage A, Yeo GS, Umrania Y, Williams G, Brenner S.
Generation and analysis of 25 Mb of genomic DNA from the pufferfish Fugu rubripes by sequence scanning. Genome Res 1999 Oct;9(10):960-71
Gallus gallus
OVERALL COORDINATION:, LADEANA W. HILLIER1, WEBB MILLER, EWAN BIRNEY, WESLEY WARREN, ROSS C. HARDISON, CHRIS P. PONTING, PEER BORK, DAVID W. BURT, MARTIEN A. M. GROENEN, MARY E. DELANY, JERRY B. DODGSON, GENOME FINGERPRINT MAP, SEQUENCE AND ASSEMBLY:, ASIF T. CHINWALLA, PAUL F. CLIFTEN, SANDRA W. CLIFTON, KIMBERLY D. DELEHAUNTY, CATRINA FRONICK, ROBERT S. FULTON, TINA A. GRAVES, COLIN KREMITZKI, DAN LAYMAN, VINCENT MAGRINI, JOHN D. MCPHERSON1, TRACIE L. MINER, PATRICK MINX, WILLIAM E. NASH, MICHAEL N. NHAN, JOANNE O. NELSON, LACHLAN G. ODDY, CRAIG S. POHL, JENNIFER RANDALL-MAHER, SCOTT M. SMITH, JOHN W. WALLIS, SHIAW-PYNG YANG, MAPPING :, MICHAEL N. ROMANOV, CATHERINE M. RONDELLI, BOB PATON, JACQUELINE SMITH, DAVID MORRICE, LAURA DANIELS, HELEN G. TEMPEST, LINDSAY ROBERTSON, JULIO S. MASABANDA, DARREN K. GRIFFIN, ALAIN VIGNAL, VALERIE FILLON, LINA JACOBBSON, SUSANNE KERJE, LEIF ANDERSSON, RICHARD P. M. CROOIJMANS, JAN AERTS, JAN J. VAN DER POEL, HANS ELLEGREN, CDNA SEQUENCING:, RANDOLPH B. CALDWELL, SIMON J. HUBBARD, DARREN V. GRAFHAM, ANDRZEJ M. KIERZEK, STUART R. MCLAREN, IAN M. OVERTON, HIROSHI ARAKAWA, KEVIN J. BEATTIE, YURI BEZZUBOV, PAUL E. BOARDMAN, JAMES K. BONFIELD, MICHAEL D. R. CRONING, ROBERT M. DAVIES, MATTHEW D. FRANCIS, SEAN J. HUMPHRAY, CAROL E. SCOTT, RUTH G. TAYLOR, CHERYLL TICKLE, WILLIAM R. A. BROWN, JANE ROGERS, JEAN-MARIE BUERSTEDDE, STUART A. WILSON, OTHER SEQUENCING AND LIBRARIES:, LISA STUBBS, IVAN OVCHARENKO, LAURIE GORDON, SUSAN LUCAS, MARCIA M. MILLER, HIDETOSHI INOKO, TAKASHI SHIINA, JIM KAUFMAN, JAN SALOMONSEN, KARSTEN SKJOEDT, GANE KA-SHU WONG, JUN WANG, BIN LIU, JIAN WANG, JUN YU, HUANMING YANG, MIKHAIL NEFEDOV, MAXIM KORIABINE, PIETER J. DEJONG, ANALYSIS AND ANNOTATION:, LEO GOODSTADT, CALEB WEBBER, NICHOLAS J. DICKENS, IVICA LETUNIC, MIKITA SUYAMA, DAVID TORRENTS, CHRISTIAN VON MERING, EVGENY M. ZDOBNOV, KATERYNA MAKOVA, ANTON NEKRUTENKO, LAURA ELNITSKI, PALLAVI ESWARA, DAVID C. KING, SHAN YANG, SVITLANA TYEKUCHEVA, ANUSHA RADAKRISHNAN, ROBERT S. HARRIS, FRANCESCA CHIAROMONTE, JAMES TAYLOR, JIANBIN HE, MONIQUE RIJNKELS, SAM GRIFFITHS-JONES, ABEL URETA-VIDAL, MICHAEL M. HOFFMAN, JESSICA SEVERIN, STEPHEN M. J. SEARLE, ANDY S. LAW, DAVID SPEED, DAVE WADDINGTON, ZE CHENG, ERAY TUZUN, EVAN EICHLER, ZHIRONG BAO, PAUL FLICEK, DAVID D. SHTEYNBERG, MICHAELR. BRENT, JACQUELINE M. BYE, ELIZABETH J. HUCKLE, SOURAV CHATTERJI, COLIN DEWEY, LIOR PACHTER, ANDREI KOURANOV, ZISSIMOS MOURELATOS, ARTEMIS G. HATZIGEORGIOU, ANDREW H. PATERSON, ROBERT IVARIE, MIKAEL BRANDSTROM, ERIK AXELSSON, NICLAS BACKSTROM, SOFIA BERLIN, MATTHEW T. WEBSTER, OLIVIER POURQUIE, ALEXANDRE REYMOND, CATHERINE UCLA, STYLIANOS E. ANTONARAKIS, MANYUAN LONG, J. J. EMERSON, ESTHER BETRN, ISABELLE DUPANLOUP, HENRIK KAESSMANN, ANGIE S. HINRICHS, GILL BEJERANO, TERRENCE S. FUREY, RACHEL A. HARTE, BRIAN RANEY, ADAM SIEPEL, W. JAMES KENT, DAVID HAUSSLER, EDUARDO EYRAS, ROBERT CASTELO, JOSEP F. ABRIL, SERGI CASTELLANO, FRANCISCO CAMARA, GENIS PARRA, RODERIC GUIGO, GUILLAUME BOURQUE, GLENN TESLER, PAVEL A. PEVZNER, ARIAN SMIT, PROJECT MANAGEMENT:, LUCINDA A. FULTON, ELAINE R. MARDIS & RICHARD K. WILSON
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution Nature 432, 695 - 716 (09 December 2004); doi:10.1038/nature03154
(GROUP CONTRIBUTIONS ARE LISTED BY THEIR ORDER OF APPEARANCE IN THE MANUSCRIPT.), POLYMORPHISM DISCOVERY AND ANALYSIS: BEIJING INSTITUTE OF GENOMICS OF CHINESE ACADEMY OF SCIENCES AND JAMES D. WATSON INSTITUTE OF GENOME SCIENCES OF ZHEJIANG UNIVERSITY, GANE KA-SHU WONG, BIN LIU, JUN WANG, YONG ZHANG, XU YANG, ZENGJIN ZHANG, QINGSHUN MENG, JUN ZHOU, DAWEI LI, JINGJING ZHANG, PEIXIANG NI, SONGGANG LI, LONGHUA RAN, HENG LI, JIANGUO ZHANG, RUIQIANG LI, SHENGTING LI, HONGKUN ZHENG, WEI LIN, GUANGYUAN LI, XIAOLING WANG, WENMING ZHAO, JUN LI, CHEN YE, MINGTAO DAI, JUE RUAN, YAN ZHOU, YUANZHE LI, XIMIAO HE, YUNZE ZHANG, JING WANG, XIANGANG HUANG, WEI TONG, JIE CHEN, JIA YE, CHEN CHEN, NING WEI, GUOQING LI, LE DONG, FENGDI LAN, YONGQIAO SUN, ZHENPENG ZHANG, ZHENG YANG, YINGPU YU, YANQING HUANG, DANDAN HE, YAN XI, DONG WEI, QIUHUI QI, WENJIE LI, JIANPING SHI, MIAOHENG WANG, FEI XIE, JIANJUN WANG, XIAOWEI ZHANG, PEI WANG, YIQIANG ZHAO, NING LI, NING YANG, WEI DONG, SONGNIAN HU, CHANGQING ZENG, WEIMOU ZHENG, BAILIN HAO, GENOME SEQUENCE OF RED JUNGLE FOWL: WASHINGTON UNIVERSITY SCHOOL OF MEDICINE, LADEANA W. HILLIER, SHIAW-PYNG YANG, WESLEY C. WARREN, RICHARD K. WILSON, MOLECULAR EVOLUTION: UPPSALA UNIVERSITY, MIKAEL BRANDSTRM, HANS ELLEGREN, POPULATION GENOTYPING, BAC SEQUENCES AND HAPLOTYPES: WAGENINGEN UNIVERSITY, RICHARD P. M. A. CROOIJMANS, JAN J. VAN DER POEL, HENK BOVENHUIS, MARTIEN A. M. GROENEN, LAWRENCE LIVERMORE NATIONAL LABORATORY, IVAN OVCHARENKO, LAURIE GORDON, LISA STUBBS, DOE JOINT GENOME INSTITUTE, SUSAN LUCAS, TIJANA GLAVINA, ANDREA AERTS, EXAMPLES OF APPLICATION TO COMPLEX TRAITS: INSTITUTE FOR ANIMAL HEALTH, PETE KAISER, LISA ROTHWELL, JOHN R. YOUNG, SALLY ROGERS, BRIAN A. WALKER, ANDY VAN HATEREN, JIM KAUFMAN, NAT BUMSTEAD, IOWA STATE UNIVERSITY, SUSAN J. LAMONT, HUAIJUN ZHOU, ROSLIN INSTITUTE, PAUL M. HOCKING, DAVID MORRICE, DIRK-JAN DE KONING, ANDY LAW, NEIL BARTLEY, DAVID W. BURT, USDA-ARS AVIAN DISEASE AND ONCOLOGY LABORATORY, HENRY HUNT, HANS H. CHENG, DOMESTICATION AND SELECTION: UPPSALA UNIVERSITY, ULRIKA GUNNARSSON, PER WAHLBERG, LEIF ANDERSSON, KAROLINSKA INSTITUTET, ELLEN KINDLUND, MARTTI T. TAMMI, BJRN ANDERSSON, HUMAN DISEASE GENES: UNIVERSITY OF OXFORD, CALEB WEBBER, CHRIS P. PONTING, EST-BASED SNP DATA: UNIVERSITY OF MANCHESTER INSTITUTE OF SCIENCE AND TECHNOLOGY, IAN M. OVERTON, PAUL E BOARDMAN, HAIZHOU TANG, SIMON J. HUBBARD, UNIVERSITY OF SHEFFIELD, STUART A. WILSON, SCIENTIFIC MANAGEMENT: BEIJING INSTITUTE OF GENOMICS OF CHINESE ACADEMY OF SCIENCES, JUN YU, JIAN WANG & HUANMING YANG
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms Nature 432, 717 - 722 (09 December 2004); doi:10.1038/nature03156
Homo sapiens
Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda J, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo Mde F, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, de Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, Gopinath GR, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, Sugano S.
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol. 2004 Jun;2(6):856-75. Epub 2004 Apr 20.
Homo sapiens
Dunham I, Shimizu N, Roe BA, Chissoe S, Hunt AR, Collins JE, Bruskiewich R, Beare DM, Clamp M, Smink LJ, Ainscough R, Almeida JP, Babbage A, Bagguley C, Bailey J, Barlow K, Bates KN, Beasley O, Bird CP, Blakey S, Bridgeman AM, Buck D, Burgess J, Burrill WD, O'Brien KP, et al.
The DNA sequence of human chromosome 22. Nature 1999 Dec 2;402(6761):489-95
Ciona intestinalis
Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, Davidson B, Di Gregorio A, Gelpke M, Goodstein DM, Harafuji N, Hastings KE, Ho I, Hotta K, Huang W, Kawashima T, Lemaire P, Martinez D, Meinertzhagen IA, Necula S, Nonaka M, Putnam N, Rash S, Saiga H, Satake M, Terry A, Yamada L, Wang HG, Awazu S, Azumi K, Boore J, Branno M, Chin-Bow S, DeSantis R, Doyle S, Francino P, Keys DN, Haga S, Hayashi H, Hino K, Imai KS, Inaba K, Kano S, Kobayashi K, Kobayashi M, Lee BI, Makabe KW, Manohar C, Matassi G, Medina M, Mochizuki Y, Mount S, Morishita T, Miura S, Nakayama A, Nishizaka S, Nomoto H, Ohta F, Oishi K, Rigoutsos I, Sano M, Sasaki A, Sasakura Y, Shoguchi E, Shin-i T, Spagnuolo A, Stainier D, Suzuki MM, Tassy O, Takatori N, Tokuoka M, Yagi K, Yoshizaki F, Wada S, Zhang C, Hyatt PD, Larimer F, Detter C, Doggett N, Glavina T, Hawkins T, Richardson P, Lucas S, Kohara Y, Levine M, Satoh N, Rokhsar DS.
The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science 2002 Dec 13;298(5601):2157-67
Tetraodon nigroviridis
Grutzner F, Crollius HR, Lutjens G, Jaillon O, Weissenbach J, Ropers HH, Haaf T.
Four-hundred million years of conserved synteny of human Xp and Xq genes on three Tetraodon chromosomes. Genome Res. 2002 Sep;12(9):1316-22.
Fischer C, Ozouf-Costaz C, Roest Crollius H, Dasilva C, Jaillon O, Bouneau L, Bonillo C, Weissenbach J, Bernot A.
Karyotype and chromosome location of characteristic tandem repeats in the pufferfish Tetraodon nigroviridis. Cytogenet Cell Genet. 2000;88(1-2):50-5.
Grutzner F, Lutjens G, Rovira C, Barnes DW, Ropers HH, Haaf T.
Classical and molecular cytogenetics of the pufferfish Tetraodon nigroviridis. Chromosome Res. 1999;7(8):655-62.
Mandrioli M, Cuoghi B, Marini M, Manicardi GC.
Cytogenetic analysis of the pufferfish Tetraodon fluviatilis (Osteichthyes). Chromosome Res. 2000;8(3):237-42.
Encephalitozoon cuniculi
atinka,M.D., Duprat,S., Cornillot,E., Metenier,G., Thomarat,F., Prensier,G., Barbe,V., Peyretaillade,E., Brottier,P., Wincker,P., Delbac,F., El Alaoui,H., Peyret,P., Saurin,W., Gouy,M., Weissenbach,J. and Vivares,C.P.
Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi Nature 414 (6862), 450-453 (2001)
Cyanidioschyzon merolae
Matsuzaki M, Misumi O, Shin-I T, Maruyama S, Takahara M, Miyagishima SY, Mori T, Nishida K, Yagisawa F, Nishida K, Yoshida Y, Nishimura Y, Nakao S, Kobayashi T, Momoyama Y, Higashiyama T, Minoda A, Sano M, Nomoto H, Oishi K, Hayashi H, Ohta F, Nishizaka S, Haga S, Miura S, Morishita T, Kabeya Y, Terasawa K, Suzuki Y, Ishii Y, Asakawa S, Takano H, Ohta N, Kuroiwa H, Tanaka K, Shimizu N, Sugano S, Sato N, Nozaki H, Ogasawara N, Kohara Y, Kuroiwa T.
Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature. 2004 Apr 8;428(6983):653-7.
Chlamydomonas reinhardtii
Nozaki H, Onishi K, Morita E.
Differences in pyrenoid morphology are correlated with differences in the rbcL genes of members of the Chloromonas lineage (volvocales, chlorophyceae). J Mol Evol. 2002 Oct;55(4):414-30.
Bacteriophage T4
Pribnow,D., Sigurdson,D.C., Gold,L., Singer,B.S., Napoli,C., Brosius,J., Dull,T.J. and Noller,H.F.
rII cistrons of bacteriophage T4. DNA sequence around the intercistronic divide and positions of genetic landmarks
J Mol Biol 1981 Jul 5;149(3):337-76
Other Databases
PDB
Berman H.M., Westbrook J., Feng Z., Gilliland G.,
Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E., 2000.
The Protein Data Bank.
Nucl. Acids Res. 28, 235-242.
Swiss-prot
Bairoch A., Apweiler R., 2000.
The Swiss-Prot protein sequence database and its supplement TrEMBL in 2000.
Nucl. Acids Res. 28, 45-48.
Prosite
Hofmann K., Bucher P., Falquet L., Bairoch A.
The PROSITE database, its status in 1999
Nucleic Acids Res. 27:215-219(1999).
Pfam
Bateman A., Birney E., Durbin R., Eddy S.R., Howe K.L., Sonnhammer E.L.L., 2000.
The Pfam protein families database.
Nucl. Acids Res. 28, 263-266.
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References