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pfam database research papers

The Pfam protein families database
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ABSTRACT Pfam is a large collection of protein families and domains. Over the past 2 years the number of families in Pfam has doubled and now stands at 6190 (version 10.0). Methodology improvements for searching the Pfam collection locally as well as via the 

The Pfam protein families database
free download

ABSTRACT Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the World Wide Web in the UK at

The Pfam protein families database
free download

ABSTRACT Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. The current release of Pfam (22.0) contains 9318 protein families. Pfam is now based not only on the UniProtKB 

SledgeHMMER: a web server for batch searching the Pfam database
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ABSTRACT The SledgeHMMER web server is intended for genome-scale searching of the Pfam database without having to install this database and the HMMER software locally. The server implements a parallelized version of hmmpfam, the program used for searching the 

The Pfam protein families database
free download

ABSTRACT Pfam is a widely used database of protein families and domains. This article describes a set of major updates that we have implemented in the latest release (version 24.0). The most important change is that we now use HMMER3, the latest version of the 

The Pfam protein families database
free download

ABSTRACT Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the WWW in the UK at

The Pfam protein families database
free download

ABSTRACT Pfam is a widely used database of protein families, currently containing more than 13 000 manually curated protein families as of release 26.0. Pfam is available via servers in

ConSeq: the identification of functionally and structurally important residues in protein sequences
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 BB ,Transmembrane segment Fig. 1. ConSeq predictions demonstrated on human bestrophin (SWISS-PROT: VMD2_HUMAN), using 43 homologues obtained from the Pfam database (family code: DUF289). The sequence 

Predicting active site residue annotations in the Pfam database
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Approximately 5% of Pfam families are enzymatic, but only a small fraction of the sequences within these families have had the residues responsible for catalysis determined. To increase the active site annotations in the Pfam database, we have developed a strict set 

Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins
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Release 3.1 is a major update of the Pfam database and contains 1313 families which are available on the World Wide Web in Europe at

Pfam: multiple sequence alignments and HMM-profiles of protein domains
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The two servers are separately maintained and differ slightly in their services and capabilities, but are based on the same underlying Pfam database.  Users of the Pfam database or WWW servers should cite this article as the appropriate reference. 

Pfam: a comprehensive database of protein domain families based on seed alignments
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ABSTRACT Databases of multiple sequence alignments are a valuable aid to protein sequence classification and analysis. One of the main challenges when constructing such a database is to simultaneously satisfy the conflicting demands of completeness on the one 


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