Protein Sequence Annotation Tool (PSAT): a centralized web-based meta-server for high-throughput sequence annotations

BMC Bioinformatics
Elo LeungCarol L Ecale Zhou

Abstract

Here we introduce the Protein Sequence Annotation Tool (PSAT), a web-based, sequence annotation meta-server for performing integrated, high-throughput, genome-wide sequence analyses. Our goals in building PSAT were to (1) create an extensible platform for integration of multiple sequence-based bioinformatics tools, (2) enable functional annotations and enzyme predictions over large input protein fasta data sets, and (3) provide a web interface for convenient execution of the tools. In this paper, we demonstrate the utility of PSAT by annotating the predicted peptide gene products of Herbaspirillum sp. strain RV1423, importing the results of PSAT into EC2KEGG, and using the resulting functional comparisons to identify a putative catabolic pathway, thereby distinguishing RV1423 from a well annotated Herbaspirillum species. This analysis demonstrates that high-throughput enzyme predictions, provided by PSAT processing, can be used to identify metabolic potential in an otherwise poorly annotated genome. PSAT is a meta server that combines the results from several sequence-based annotation and function prediction codes, and is available at http://psat.llnl.gov/psat/. PSAT stands apart from other sequence-based genome annotation syst...Continue Reading

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Datasets Mentioned

BETA
CBXX010000001
CBXX010000131

Software Mentioned

Python SQLite
MetaCyc
KEGG Blast
BLAST
KEGG
Celery
MetaCyc blast
Linux
IGS
Protein Sequence Annotation tool ( PSAT )

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