Pfamデータベースとは - わかりやすく解説 Weblio辞書

Pfamデータベース

出典: フリー百科事典『ウィキペディア（Wikipedia）』 (2024/04/07 21:06 UTC 版)

Pfamは、タンパク質ファミリーのデータベースであり、アノテーションと隠れマルコフモデルを用いて生成された多重配列アライメントを含んでいる^[1]^[2]^[3]。最新版のPfam 33.1は、2020年5月にリリースされ、18,259件のファミリーを収録している^[4]。

脚注

^ Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A (2008). “The Pfam protein families database”. Nucleic Acids Res 36 (Database issue): D281–8. doi:10.1093/nar/gkm960. PMC 2238907. PMID 18039703.
^ Finn, R. D.; Mistry, J.; Schuster-Böckler, B.; Griffiths-Jones, S.; Hollich, V.; Lassmann, T.; Moxon, S.; Marshall, M. et al. (Jan 2006). “Pfam: clans, web tools and services” (Free full text). Nucleic Acids Research 34 (Database issue): D247–D251. doi:10.1093/nar/gkj149. ISSN 0305-1048. PMC 1347511. PMID 16381856.
^ Bateman, A.; Coin, L.; Durbin, R.; Finn, R. D.; Hollich, V.; Griffiths-Jones, S.; Khanna, A.; Marshall, M. et al. (2004). “The Pfam protein families database”. Nucleic Acids Research 32 (Database issue): 138D–1141. doi:10.1093/nar/gkh121. ISSN 0305-1048. PMC 308855. PMID 14681378.
^ “Pfam 31.0 is released”. Xfam Blog (2017年3月8日). 2017年3月13日閲覧。
^ ^a ^b ^c ^d Sammut, Stephen; Finn, Robert D.; Bateman, Alex (2008). “Pfam 10 years on: 10 000 families and still growing”. Briefings in Bioinformatics 9 (3): 210–219. doi:10.1093/bib/bbn010. PMID 18344544.
^ ^a ^b ^c Sonnhammer, Erik L.L.; Eddy, Sean R.; Durbin, Richard (1997). “Pfam: A Comprehensive Database of Protein Domain Families Based on Seed Alignments”. Proteins 28 (3): 405–420. doi:10.1002/(sici)1097-0134(199707)28:3<405::aid-prot10>3.0.co;2-l. PMID 9223186.
^ Xu, Qifang; Dunbrack, Roland L. (2012). “Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB”. Bioinformatics 28 (21): 2763–2772. doi:10.1093/bioinformatics/bts533. PMC 3476341. PMID 22942020.
^ ^a ^b ^c Finn, R. D.; Mistry, J.; Tate, J.; Coggill, P.; Heger, A.; Pollington, J. E.; Gavin, O. L.; Gunasekaran, P. et al. (2009). “The Pfam protein families database”. Nucleic Acids Research 38 (Database): D211–D222. doi:10.1093/nar/gkp985. ISSN 0305-1048. PMC 2808889. PMID 19920124.
^ ^a ^b Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL (2002). “The Pfam protein families database”. Nucleic Acids Res. 30 (1): 276–80. doi:10.1093/nar/30.1.276. PMC 99071. PMID 11752314.
^ Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, George RA, Lewis SE, Richards S, Ashburner M, Henderson SN, Sutton GG, Wortman JR, Yandell MD, Zhang Q, Chen LX, Brandon RC, Rogers YH, Blazej RG, Champe M, Pfeiffer BD, Wan KH, Doyle C, Baxter EG, Helt G, Nelson CR, Gabor GL, Abril JF, Agbayani A, An HJ, Andrews-Pfannkoch C, Baldwin D, Ballew RM, Basu A, Baxendale J, Bayraktaroglu L, Beasley EM, Beeson KY, Benos PV, Berman BP, Bhandari D, Bolshakov S, Borkova D, Botchan MR, Bouck J, Brokstein P, Brottier P, Burtis KC, Busam DA, Butler H, Cadieu E, Center A, Chandra I, Cherry JM, Cawley S, Dahlke C, Davenport LB, Davies P, de Pablos B, Delcher A, Deng Z, Mays AD, Dew I, Dietz SM, Dodson K, Doup LE, Downes M, Dugan-Rocha S, Dunkov BC, Dunn P, Durbin KJ, Evangelista CC, Ferraz C, Ferriera S, Fleischmann W, Fosler C, Gabrielian AE, Garg NS, Gelbart WM, Glasser K, Glodek A, Gong F, Gorrell JH, Gu Z, Guan P, Harris M, Harris NL, Harvey D, Heiman TJ, Hernandez JR, Houck J, Hostin D, Houston KA, Howland TJ, Wei MH, Ibegwam C, Jalali M, Kalush F, Karpen GH, Ke Z, Kennison JA, Ketchum KA, Kimmel BE, Kodira CD, Kraft C, Kravitz S, Kulp D, Lai Z, Lasko P, Lei Y, Levitsky AA, Li J, Li Z, Liang Y, Lin X, Liu X, Mattei B, McIntosh TC, McLeod MP, McPherson D, Merkulov G, Milshina NV, Mobarry C, Morris J, Moshrefi A, Mount SM, Moy M, Murphy B, Murphy L, Muzny DM, Nelson DL, Nelson DR, Nelson KA, Nixon K, Nusskern DR, Pacleb JM, Palazzolo M, Pittman GS, Pan S, Pollard J, Puri V, Reese MG, Reinert K, Remington K, Saunders RD, Scheeler F, Shen H, Shue BC, Sidén-Kiamos I, Simpson M, Skupski MP, Smith T, Spier E, Spradling AC, Stapleton M, Strong R, Sun E, Svirskas R, Tector C, Turner R, Venter E, Wang AH, Wang X, Wang ZY, Wassarman DA, Weinstock GM, Weissenbach J, Williams SM, WoodageT, Worley KC, Wu D, Yang S, Yao QA, Ye J, Yeh RF, Zaveri JS, Zhan M, Zhang G, Zhao Q, Zheng L, Zheng XH, Zhong FN, Zhong W, Zhou X, Zhu S, Zhu X, Smith HO, Gibbs RA, Myers EW, Rubin GM, Venter JC (2000). “The genome sequence of Drosophila melanogaster”. Science 287 (5461): 2185–95. Bibcode: 2000Sci...287.2185.. doi:10.1126/science.287.5461.2185. PMID 10731132.
^ Lander, Eric S.; Linton, Lauren M.; Birren, Bruce; Nusbaum, Chad; Zody, Michael C. et al. (2001). “Initial sequencing and analysis of the human genome”. Nature 409 (6822): 860–921. doi:10.1038/35057062. ISSN 0028-0836. PMID 11237011.
^ Finn, Robert D.; Bateman, Alex; Clements, Jody; Coggill, Penelope; Eberhardt, Ruth Y.; Eddy, Sean R.; Heger, Andreas; Hetherington, Kirstie et al. (2014). “Pfam: the protein families database”. Nucleic Acids Research 42 (D1): D222–D230. doi:10.1093/nar/gkt1223. ISSN 0305-1048. PMC 3965110. PMID 24288371.
^ Sonnhammer EL, Eddy SR, Birney E, Bateman A, Durbin R (1998). “Pfam: multiple sequence alignments and HMM-profiles of protein domains”. Nucleic Acids Res. 26 (1): 320–2. doi:10.1093/nar/26.1.320. PMC 147209. PMID 9399864.
^ Finn, R. D.; Marshall, M.; Bateman, A. (2004). “iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions”. Bioinformatics 21 (3): 410–412. doi:10.1093/bioinformatics/bti011. ISSN 1367-4803. PMID 15353450.
^ ^a ^b ^c ^d Finn, Robert D.; Coggill, Penelope; Eberhardt, Ruth Y.; Eddy, Sean R.; Mistry, Jaina; Mitchell, Alex L.; Potter, Simon C.; Punta, Marco et al. (2016). “The Pfam protein families database: towards a more sustainable future”. Nucleic Acids Research 44 (D1): D279–D285. doi:10.1093/nar/gkv1344. ISSN 0305-1048. PMC 4702930. PMID 26673716.
^ ^a ^b ^c ^d ^e ^f Punta, M.; Coggill, P. C.; Eberhardt, R. Y.; Mistry, J.; Tate, J.; Boursnell, C.; Pang, N.; Forslund, K. et al. (2011). “The Pfam protein families database”. Nucleic Acids Research 40 (D1): D290–D301. doi:10.1093/nar/gkr1065. ISSN 0305-1048. PMC 3245129. PMID 22127870.
^ ^a ^b El-Gebali, Sara; Mistry, Jaina; Bateman, Alex; Eddy, Sean R; Luciani, Aurélien; Potter, Simon C; Qureshi, Matloob; Richardson, Lorna J et al. (8 January 2019). “The Pfam protein families database in 2019”. Nucleic Acids Research 47 (D1): D427–D432. doi:10.1093/nar/gky995. PMC 6324024. PMID 30357350.
^ “Evolutionary Classification of Protein Domains”. prodata.swmed.edu. 2019年5月18日閲覧。
^ Chothia, Cyrus (1992). “One thousand families for the molecular biologist”. Nature 357 (6379): 543–544. Bibcode: 1992Natur.357..543C. doi:10.1038/357543a0. ISSN 0028-0836. PMID 1608464.
^ Heger, A.; Wilton, C. A.; Sivakumar, A.; Holm, L. (Jan 2005). “ADDA: a domain database with global coverage of the protein universe” (Free full text). Nucleic Acids Research 33 (Database issue): D188–D191. doi:10.1093/nar/gki096. ISSN 0305-1048. PMC 540050. PMID 15608174.
^ “Pfam 28.0 release notes”. 2015年6月30日閲覧。
^ “A new Pfam-B is released” (英語). Xfam Blog (2020年6月30日). 2021年5月6日閲覧。
^ “Moving to xfam.org”. 2016年11月25日閲覧。
^ Dunbrack, Roland. “PDBfam”. Fox Chase Cancer Center. 2013年3月9日閲覧。
^ Xu, Qifang; Dunbrack, Roland (2012). “Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB”. Bioinformatics 28 (21): 2763–72. doi:10.1093/bioinformatics/bts533. PMC 3476341. PMID 22942020.

「Pfamデータベース」の続きの解説一覧

Pfamデータベースのページへのリンク

Pfamデータベースとは？わかりやすく解説

Pfamデータベース

「Pfamデータベース」の関連用語

Pfamデータベースとは？ わかりやすく解説

Pfamデータベース

急上昇のことば

「Pfamデータベース」の関連用語

Pfamデータベースとは？わかりやすく解説