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PFAAT version 2.0: A tool for editing, annotating, and analyzing multiple sequence alignments

Daniel R Caffrey1*, Paul H Dana1, Vidhya Mathur1, Marco Ocano1, Eun-Jong Hong2, Yaoyu E Wang3, Shyamal Somaroo1, Brian E Caffrey4, Shobha Potluri1 and Enoch S Huang13

Author Affiliations

1 Pfizer Global Research and Development, 620 Memorial Drive, Cambridge, MA 02139, USA

2 Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, MA 02139, USA

3 Bioinformatics Program and Biomedical Engineering Department, Boston University, MA 02215, USA

4 School of Theoretical Physics, Dublin Institute for Advanced Studies, 10 Burlington Road, Dublin 4, Ireland

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BMC Bioinformatics 2007, 8:381  doi:10.1186/1471-2105-8-381

Published: 11 October 2007



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.


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.


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.