SUPERFAMILY 1.75 HMM library and genome assignments server

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SUPERFAMILY Publications

The publications are divided into two sections:

If you use SUPERFAMILY in your work, we request that you cite one of our papers. The 2001 Journal of Molecular Biology article describes the method used to build the HMM library. The 2009 Nucleic Acids Research article describes recent SUPERFAMILY database developments. The latest publication describing SUPERFAMILY is the 2009 Nucleic Acids Research article.

Main SUPERFAMILY publications

Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure.

Gough J, Karplus K, Hughey R, Chothia C.

J Mol Biol. 2001 Nov 2;313(4):903-19.

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SUPERFAMILY - Comparative Genomics, Datamining and Sophisticated Visualisation.

Wilson D, Pethica R, Zhou Y, Talbot C, Vogel C, Madera M, Chothia C, Gough J.

Nucleic Acids Res. 2009 Jan; 37(Database issue):D380-6. Epub 2008 Nov 26.

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The SUPERFAMILY database in 2007: families and functions.

Wilson D, Madera M, Vogel C, Chothia C, Gough J.

Nucleic Acids Res. 2007 Jan;35(Database issue):D308-13. Epub 2006 Nov 10.

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The SUPERFAMILY database in 2004: additions and improvements.

Madera M, Vogel C, Kummerfeld SK, Chothia C, Gough J.

Nulceic Acids Res. 2004 Jan 1;32(Database issue):D235-9.

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SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments.

Gough J, Chothia C.

Nulceic Acids Res. 2002 Jan 1;30(1):268-72.

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The SUPERFAMILY database in structural genomics.

Gough J.

Acta Crystallogr D Biol Crystallogr. 2002 Nov;58(Pt 11):1897-900. Epub 2002 Oct 21.

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Closely related publications

Profile Comparer (PRC): a program for scoring and aligning profile hidden Markov models

Madera M

Bioinformatics 2008; doi: 10.1093/bioinformatics/btn504

Abstract [ Bioinformatics ]   Full text [ PDF ]

Genomic scale sub-family assignment of protein domains.

Gough J.

Nulceic Acids Res. 2006 Jul 28;34(13):3625-33. Print 2006.

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Data growth and its impact on the SCOP database: new developments.

Andreeva A, Howorth D, Chandonia JM, Brenner SE, Hubbard TJ, Chothia C, Murzin AG.

Nulceic Acids Res. 2008 Jan;36(Database issue):D419-25.

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The ASTRAL Compendium in 2004.

Chandonia JM, Hon G, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE.

Nulceic Acids Res. 2004 Jan 1;32(Database issue):D189-92.

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Hidden Markov models for detecting remote protein homologies.

Karplus K, Barrett C, Hughey R.

Bioinformatics. 1998;14(10):846-56.

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A comparison of profile hidden Markov model procedures for remote homology detection.

Madera M, Gough J.

Nulceic Acids Res. 2002 Oct 1;30(19):4321-8.

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