PFAAT version 2.0 : A tool for editing, annotating, and analyzing multiple sequence alignments
Background: By virtue of their shared ancestry, homologous sequences are similar in their structure and function. Consequently, multiple sequence alignments are routinely used to identify trends that relate to function. This type of analysis is particularly productive when it is combined with struct...
| Main Authors: | , , , , , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | English |
| Published: |
BioMed Central Ltd
2010
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| Online Access: | http://hdl.handle.net/1721.1/58921 |
| _version_ | 1826196857998540800 |
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| author | Caffrey, Daniel R Dana, Paul H Mathur, Vidhya Ocano, Marco Hong, Eun-Jong Wang, Yaoyu E Somaroo, Shyamal Caffrey, Brian E Potluri, Shobha Huang, Enoch S |
| author2 | Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science |
| author_facet | Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Caffrey, Daniel R Dana, Paul H Mathur, Vidhya Ocano, Marco Hong, Eun-Jong Wang, Yaoyu E Somaroo, Shyamal Caffrey, Brian E Potluri, Shobha Huang, Enoch S |
| author_sort | Caffrey, Daniel R |
| collection | MIT |
| description | Background: By virtue of their shared ancestry, homologous sequences are similar in their structure and function. Consequently, multiple sequence alignments are routinely used to identify trends that relate to function. This type of analysis is particularly productive when it is combined with structural and phylogenetic analysis. Results: Here we describe the release of PFAAT version 2.0, a tool for editing, analyzing, and annotating multiple sequence alignments. Support for multiple annotations is a key component of this release as it provides a framework for most of the new functionalities. The sequence annotations are accessible from the alignment and tree, where they are typically used to label sequences or hyperlink them to related databases. Sequence annotations can be created manually or extracted automatically from UniProt entries. Once a multiple sequence alignment is populated with sequence annotations, sequences can be easily selected and sorted through a sophisticated search dialog. The selected sequences can be further analyzed using statistical methods that explicitly model relationships between the sequence annotations and residue properties. Residue annotations are accessible from the alignment viewer and are typically used to designate binding sites or properties for a particular residue. Residue annotations are also searchable, and allow one to quickly select alignment columns for further sequence analysis, e.g. computing percent identities. Other features include: novel algorithms to compute sequence conservation, mapping conservation scores to a 3D structure in Jmol, displaying secondary structure elements, and sorting sequences by residue composition. Conclusion: PFAAT provides a framework whereby end-users can specify knowledge for a protein family in the form of annotation. The annotations can be combined with sophisticated analysis to test hypothesis that relate to sequence, structure and function. |
| first_indexed | 2024-09-23T10:39:05Z |
| format | Article |
| id | mit-1721.1/58921 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T10:39:05Z |
| publishDate | 2010 |
| publisher | BioMed Central Ltd |
| record_format | dspace |
| spelling | mit-1721.1/589212022-09-27T13:58:55Z PFAAT version 2.0 : A tool for editing, annotating, and analyzing multiple sequence alignments Caffrey, Daniel R Dana, Paul H Mathur, Vidhya Ocano, Marco Hong, Eun-Jong Wang, Yaoyu E Somaroo, Shyamal Caffrey, Brian E Potluri, Shobha Huang, Enoch S Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Hong, Eun-Jong Background: By virtue of their shared ancestry, homologous sequences are similar in their structure and function. Consequently, multiple sequence alignments are routinely used to identify trends that relate to function. This type of analysis is particularly productive when it is combined with structural and phylogenetic analysis. Results: Here we describe the release of PFAAT version 2.0, a tool for editing, analyzing, and annotating multiple sequence alignments. Support for multiple annotations is a key component of this release as it provides a framework for most of the new functionalities. The sequence annotations are accessible from the alignment and tree, where they are typically used to label sequences or hyperlink them to related databases. Sequence annotations can be created manually or extracted automatically from UniProt entries. Once a multiple sequence alignment is populated with sequence annotations, sequences can be easily selected and sorted through a sophisticated search dialog. The selected sequences can be further analyzed using statistical methods that explicitly model relationships between the sequence annotations and residue properties. Residue annotations are accessible from the alignment viewer and are typically used to designate binding sites or properties for a particular residue. Residue annotations are also searchable, and allow one to quickly select alignment columns for further sequence analysis, e.g. computing percent identities. Other features include: novel algorithms to compute sequence conservation, mapping conservation scores to a 3D structure in Jmol, displaying secondary structure elements, and sorting sequences by residue composition. Conclusion: PFAAT provides a framework whereby end-users can specify knowledge for a protein family in the form of annotation. The annotations can be combined with sophisticated analysis to test hypothesis that relate to sequence, structure and function. 2010-10-06T20:07:56Z 2010-10-06T20:07:56Z 2007-10 2007-08 2010-09-03T16:14:26Z Article http://purl.org/eprint/type/JournalArticle 1471-2105 http://hdl.handle.net/1721.1/58921 BMC Bioinformatics. 2007 Oct 11;8(1):381 17931421 en http://dx.doi.org/10.1186/1471-2105-8-381 BMC bioinformatics Creative Commons Attribution http://creativecommons.org/licenses/by/2.0 Caffrey et al.; licensee BioMed Central Ltd. application/pdf BioMed Central Ltd BioMed Central Ltd |
| spellingShingle | Caffrey, Daniel R Dana, Paul H Mathur, Vidhya Ocano, Marco Hong, Eun-Jong Wang, Yaoyu E Somaroo, Shyamal Caffrey, Brian E Potluri, Shobha Huang, Enoch S PFAAT version 2.0 : A tool for editing, annotating, and analyzing multiple sequence alignments |
| title | PFAAT version 2.0 : A tool for editing, annotating, and analyzing multiple sequence alignments |
| title_full | PFAAT version 2.0 : A tool for editing, annotating, and analyzing multiple sequence alignments |
| title_fullStr | PFAAT version 2.0 : A tool for editing, annotating, and analyzing multiple sequence alignments |
| title_full_unstemmed | PFAAT version 2.0 : A tool for editing, annotating, and analyzing multiple sequence alignments |
| title_short | PFAAT version 2.0 : A tool for editing, annotating, and analyzing multiple sequence alignments |
| title_sort | pfaat version 2 0 a tool for editing annotating and analyzing multiple sequence alignments |
| url | http://hdl.handle.net/1721.1/58921 |
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