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Domain annotation of trimeric autotransporter adhesins--daTAA.

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

SUBMITTER: Szczesny P

PROVIDER: S-EPMC2373917 | biostudies-literature | 2008 May

REPOSITORIES: biostudies-literature

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Domain annotation of trimeric autotransporter adhesins--daTAA.

Szczesny Pawel P Lupas Andrei A

Bioinformatics (Oxford, England) 20080408 10

<h4>Motivation</h4>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 ...[more]

PMID: 18397894

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