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. 2008 Sep:Chapter 2:2.5.1-2.5.17.
doi: 10.1002/0471250953.bi0205s23.

Identifying protein domains with the Pfam database

Penny Coggill  1 , Robert D Finn  1 , Alex Bateman  1
Affiliations

Identifying protein domains with the Pfam database

Penny Coggill et al. Curr Protoc Bioinformatics. 2008 Sep.

Abstract

Pfam is a database of protein domain families, with each family represented by multiple sequence alignments and profile hidden Markov models (HMMs). In addition, each family has associated annotation, literature references, and links to other databases. The entries in Pfam are available via the World Wide Web and in flatfile format. This unit contains detailed information on how to access and utilize the information present in the Pfam database, namely the families, multiple alignments, and annotation. Details on running Pfam, both remotely and locally are presented.

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References

Literature Cited

    1. Bateman, A., Birney, E., Cerrutti, L., Durbin, R., Etwiller, L., Eddy, S.R., Griffiths-Jones, S., Howe, K.L., Marshall, M., and Sonnhammer, E.L. 2002. The Pfam protein families database. Nucleic Acids Res. 30: 276-280.
    1. Birney, E., Clamp, M., and Durbin, R. 2004. GeneWise and Genomewise. Genome Res. 14: 998-995.
    1. Chothia, C. 1992. Proteins. One thousand families for the molecular biologist. Nature 357: 543-534.
    1. Corpet, F., Servant, F., Gouzy, J., and Kahn, D. 2000. ProDom and ProDom-CG: Tools for protein domain analysis and whole genome comparisons. Nucleic Acids Res. 28: 267-269.
    1. Finn, R.D., Tate, J., Mistry, J., Coggill, P.C., Sammut, S.J., Hotz, H.R., Ceric, G., Forslund, K., Eddy, S.R., Sonnhammer, E.L.L., and Bateman, A. 2008. The Pfam protein families database. Nucleic Acids Res. 36: D281-D288.

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