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Bioinformatics Advance Access originally published online on April 8, 2008
Bioinformatics 2008 24(10):1251-1256; doi:10.1093/bioinformatics/btn118
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Domain annotation of trimeric autotransporter adhesins—daTAA

Pawel Szczesny 1,2 and Andrei Lupas 1,*

1Department of Protein Evolution, Max-Planck Institute for Developmental Biology, Spemannstr 35, 72076 Tuebingen, Germany and 2Department of Bioinformatics, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland

*To whom correspondence should be addressed.


  Abstract

Motivation: Trimeric autotransporter adhesins (TAAs), such as Yersinia YadA, Neisseria NadA, Moraxella UspAs, Haemophilus Hia and Bartonella BadA, are important pathogenicity factors of proteobacteria. Their high sequence diversity and distinct mosaic-like structure lead to difficulties in the annotation of their sequences. These stem from the large number of short repeats, the presence of compositionally unusual coiled-coils, fuzzy domain boundaries and regions of seemingly low sequence complexity.

Results: We have developed a workflow, named daTAA, for the accurate domain annotation of TAAs. Its core consists of manually curated alignments and of knowledge-based rules that enhance assignments made by sequence similarity. Compared to general domain annotation servers such as PFAM, daTAA captures more domains and provides more sensitive domain detection, as well as integrated and detailed coiled-coil assignments.

Availability: The daTAA server is freely accessible at http://toolkit.tuebingen.mpg.de/dataa

Contact: andrei.lupas{at}tuebingen.mpg.de

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Alfonso Valencia

Received on November 21, 2007; revised on March 27, 2008; accepted on March 31, 2008

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