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ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes
Thomas Dan Otto1, Marcos Catanho, Cristian Tristão
1Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil. otto@fiocruz.br
Bioinformatics (Oxford, England)
|January 22, 2010
Summary
ProteinWorldDB offers accurate, all-against-all protein sequence comparisons for biological research. This extensive dataset, generated using the Smith-Waterman algorithm, aids functional and evolutionary inferences.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Biological sequence comparison is crucial for functional, evolutionary, and structural inferences in modern research.
- Heuristic methods in large-scale sequence comparisons often lack accuracy.
- ProteinWorldDB addresses these limitations by providing a comprehensive, rigorously computed dataset.
Purpose of the Study:
- To create a reliable and consistent dataset of all-against-all protein sequence comparisons.
- To improve and validate results from large-scale biological sequence analyses.
- To make an extensive protein alignment database accessible for research.
Main Methods:
- Performed all-against-all comparisons of 4 million protein sequences from the RefSeq database.
- Utilized an implementation of the Smith-Waterman algorithm for rigorous dynamic programming.
- Leveraged World Community Grid for intensive computational analysis via the Genome Comparison Project.
Main Results:
- Generated ProteinWorldDB, containing pairwise protein alignment coordinates and scores.
- The database integrates annotations from Swiss-Prot, Pfam, KEGG, NCBI Taxonomy, and Gene Ontology.
- Enables users to download, compare, and analyze results filtered by genomes, functions, or clusters.
Conclusions:
- ProteinWorldDB is a unique resource for cross-comparisons of protein content across hundreds of sequenced genomes.
- Provides a valuable asset for enhancing the accuracy of functional, evolutionary, and structural inferences.
- Facilitates advanced biological research through accessible, high-quality comparative data.
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