Literature and Links to sites mentioned in Lecture 7
Literature
PSSM Position-based sequence weights.
Henikoff S and Henikoff JG4)
J Mol Biol 1994 Nov 4;243(4):574-8
Prosite PROSITE: a documented database using patterns and profiles as motif descriptors.
Sigrist CJ, Cerutti L, Hulo N, Gattiker A, Falquet L, Pagni M, Bairoch A, Bucher P.
Brief Bioinform 2002 Sep;3(3):265-74
PROSITE, a protein domain database for functional characterization and annotation.
Sigrist CJA, Cerutti L, de Castro E, Langendijk-Genevaux PS, Bulliard V, Bairoch A, Hulo N.
Nucleic Acids Res. 38(Database issue)161-6 (2010).
Pfam The Pfam Protein Families Database
Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunesekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A
Nucleic Acids Res. 2010 Jan 1;32(Database issue):D138-41.
Interpro InterPro: the integrative protein signature database
Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJA, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, and Yeats C
Nucleic Acids Res 2009 37 (Database Issue):D211-D215
SMART SMART, a simple modular architecture research tool: identification of signaling domains.
Schultz J, Milpetz F, Bork P, Ponting CP.
PNAS. 1998 May 26;95(11):5857-64.
Prints PRINTS and PRINTS-S shed light on protein ancestry
Attwood TK, Blythe MJ, Flower DR, Gaulton A, Mabey JE, Maudling N, McGregor L, Mitchell AL, Moulton G, Paine K, Scordis P.
Nucleic Acids Res 2002 Jan 1;30(1):239-41
Panther The PANTHER database of protein families, subfamilies, functions and pathways.
Mi H, Lazareva-Ulitsky B, Loo R, Kejariwal A, Vandergriff J, Rabkin S, Guo N, Muruganujan A, Doremieux O, Campbell MJ, Kitano H, Thomas PD.
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D284-8.
ProDom ProDom: Automated clustering of homologous domains.
Servant F, Bru C, Carrire S, Courcelle E, Gouzy J, Peyruc D, Kahn D
Briefings in Bioinformatics. 2002 3(3):246-251
TIGRFAM The TIGRFAMs database of protein families.
Haft DH, Selengut JD, White O.
Nucleic Acids Res. 2003 Jan 1;31(1):371-3.
Blocks The Blocks database--a system for protein classification.
Pietrokovski S, Henikoff JG, Henikoff S
Nucleic Acids Res. 1996 Jan 1;24(1):197-200
PSI-Blast Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ
Nucleic Acids Res 1997 Sep 1;25(17):3389-402