Limits...
The Pfam protein families database.

Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A - Nucleic Acids Res. (2007)

Bottom Line: 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 sequence database, but also on NCBI GenPept and on sequences from selected metagenomics projects.

View Article: PubMed Central - PubMed

Affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton Hall, Hinxton, Cambridgeshire, CB10 1SA, UK.

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 sequence database, but also on NCBI GenPept and on sequences from selected metagenomics projects. Pfam is available on the web from the consortium members using a new, consistent and improved website design in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/), as well as from mirror sites in France (http://pfam.jouy.inra.fr/) and South Korea (http://pfam.ccbb.re.kr/).

Show MeSH
The DAS-based Pfam sequence alignment viewer. A portion of the Piwi domain full alignment is shown with residue conservation highlighted in a ClustalX (19) style colour scheme.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2238907&req=5

Figure 3: The DAS-based Pfam sequence alignment viewer. A portion of the Piwi domain full alignment is shown with residue conservation highlighted in a ClustalX (19) style colour scheme.

Mentions: Another use of DAS within the new website is in the Pfam sequence alignment viewer. Pfam provides two alignments for every family: the seed alignment is a manually curated alignment of related sequences and generally contains a relatively small number of sequences; the full alignment is generated by searching the sequence database using the HMM for the family and may contain a very large number of sequences (the largest alignment, that of GP120, currently contains over 68 000 sequences). Historically, it has been difficult, if not impossible, to view the largest sequence alignments in a web browser, due simply to the size of the resulting web page. We have implemented a DAS-based sequence alignment viewer (shown in Figure 3) that is able to present even the largest alignments in manageable portions, by retrieving only the required section of the alignment and rendering it as HTML. This allows the user to scroll through wide alignments (those with long sequences) or to page through long alignments (those with a large number of sequences), without having to load the entire alignment into their browser. Alignments are coloured according to a pre-calculated consensus sequence, which is also retrieved via DAS, and in this way even alignment fragments can be marked-up using the properties of the whole alignment.Figure 3.


The Pfam protein families database.

Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A - Nucleic Acids Res. (2007)

The DAS-based Pfam sequence alignment viewer. A portion of the Piwi domain full alignment is shown with residue conservation highlighted in a ClustalX (19) style colour scheme.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238907&req=5

Figure 3: The DAS-based Pfam sequence alignment viewer. A portion of the Piwi domain full alignment is shown with residue conservation highlighted in a ClustalX (19) style colour scheme.
Mentions: Another use of DAS within the new website is in the Pfam sequence alignment viewer. Pfam provides two alignments for every family: the seed alignment is a manually curated alignment of related sequences and generally contains a relatively small number of sequences; the full alignment is generated by searching the sequence database using the HMM for the family and may contain a very large number of sequences (the largest alignment, that of GP120, currently contains over 68 000 sequences). Historically, it has been difficult, if not impossible, to view the largest sequence alignments in a web browser, due simply to the size of the resulting web page. We have implemented a DAS-based sequence alignment viewer (shown in Figure 3) that is able to present even the largest alignments in manageable portions, by retrieving only the required section of the alignment and rendering it as HTML. This allows the user to scroll through wide alignments (those with long sequences) or to page through long alignments (those with a large number of sequences), without having to load the entire alignment into their browser. Alignments are coloured according to a pre-calculated consensus sequence, which is also retrieved via DAS, and in this way even alignment fragments can be marked-up using the properties of the whole alignment.Figure 3.

Bottom Line: 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 sequence database, but also on NCBI GenPept and on sequences from selected metagenomics projects.

View Article: PubMed Central - PubMed

Affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton Hall, Hinxton, Cambridgeshire, CB10 1SA, UK.

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 sequence database, but also on NCBI GenPept and on sequences from selected metagenomics projects. Pfam is available on the web from the consortium members using a new, consistent and improved website design in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/), as well as from mirror sites in France (http://pfam.jouy.inra.fr/) and South Korea (http://pfam.ccbb.re.kr/).

Show MeSH