Protein family neighborhood analyzer-ProFaNA

Baranowski, Bartosz (author): Warsaw University of Life Sciences,Institute of Biochemistry and Biophysics of the Polish Academy of Sciences

Pawłowski, Krzysztof (author): Lund University,Lunds universitet,Klinisk kemi, Malmö,Forskargrupper vid Lunds universitet,Clinical Protein Science and Imaging,Clinical Chemistry, Malmö,Lund University Research Groups,University of Texas Southwestern Medical Center,Warsaw University of Life Sciences

(creator_code:org_t)

Related links:: http://dx.doi.org/10... (free); show more...; https://lup.lub.lu.s...; https://doi.org/10.7...; show less...

Abstract Subject headings

Background: Functionally related genes are well known to be often grouped in close vicinity in the genomes, particularly in prokaryotes. Notwithstanding the diverse evolutionary mechanisms leading to this phenomenon, it can be used to predict functions of uncharacterized genes. Methods: Here, we provide a simple but robust statistical approach that leverages the vast amounts of genomic data available today. Considering a protein domain as a functional unit, one can explore other functional units (domains) that significantly often occur within the genomic neighborhoods of the queried domain. This analysis can be performed across different taxonomic levels. Provisions can also be made to correct for the uneven sampling of the taxonomic space by genomic sequencing projects that often focus on large numbers of very closely related strains, e.g., pathogenic ones. To this end, an optional procedure for averaging occurrences within subtaxa is available. Results: Several examples show this approach can provide useful functional predictions for uncharacterized gene families, and how to combine this information with other approaches. The method is made available as a web server at http://bioinfo.sggw.edu.pl/neighborhood_analysis.

About the subject

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Bioinformatics a ...

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