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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 Pfam protein sequence page, showing the DAS annotation viewer. Various tracks can be selected using the check boxes beneath the annotation view, allowing the user to view features derived from any of the listed DAS sources. For instance, in the example displayed, the membrane topology calculated by Phobius (18) can be viewed alongside the Pfam domain annotations and those from a variety of different domain databases. The figure shows a tool-tip for one feature, which gives the details of the annotation and, in this case, highlights the link to further information.
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Figure 2: The Pfam protein sequence page, showing the DAS annotation viewer. Various tracks can be selected using the check boxes beneath the annotation view, allowing the user to view features derived from any of the listed DAS sources. For instance, in the example displayed, the membrane topology calculated by Phobius (18) can be viewed alongside the Pfam domain annotations and those from a variety of different domain databases. The figure shows a tool-tip for one feature, which gives the details of the annotation and, in this case, highlights the link to further information.

Mentions: We have also been able to incorporate other data sources that are accessible through DAS, in order to enrich our own display of Pfam data. One feature of the new website is a DAS-based viewer for sequence annotations (Figure 2). This allows the user to view annotations of protein sequences from a wide range of third-party databases alongside information from Pfam itself. The viewer presents the standard Pfam domain structure image, showing the arrangement of Pfam domains on the sequence in question, and allows users to add or hide annotations from any of the available DAS sources. As the user moves their mouse over each feature, a tool-tip gives detailed information about it. If provided by the external DAS source, a link to further information is also given.Figure 2.


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 Pfam protein sequence page, showing the DAS annotation viewer. Various tracks can be selected using the check boxes beneath the annotation view, allowing the user to view features derived from any of the listed DAS sources. For instance, in the example displayed, the membrane topology calculated by Phobius (18) can be viewed alongside the Pfam domain annotations and those from a variety of different domain databases. The figure shows a tool-tip for one feature, which gives the details of the annotation and, in this case, highlights the link to further information.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 2: The Pfam protein sequence page, showing the DAS annotation viewer. Various tracks can be selected using the check boxes beneath the annotation view, allowing the user to view features derived from any of the listed DAS sources. For instance, in the example displayed, the membrane topology calculated by Phobius (18) can be viewed alongside the Pfam domain annotations and those from a variety of different domain databases. The figure shows a tool-tip for one feature, which gives the details of the annotation and, in this case, highlights the link to further information.
Mentions: We have also been able to incorporate other data sources that are accessible through DAS, in order to enrich our own display of Pfam data. One feature of the new website is a DAS-based viewer for sequence annotations (Figure 2). This allows the user to view annotations of protein sequences from a wide range of third-party databases alongside information from Pfam itself. The viewer presents the standard Pfam domain structure image, showing the arrangement of Pfam domains on the sequence in question, and allows users to add or hide annotations from any of the available DAS sources. As the user moves their mouse over each feature, a tool-tip gives detailed information about it. If provided by the external DAS source, a link to further information is also given.Figure 2.

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