Document Type

Article

Rights

This item is available under a Creative Commons License for non-commercial use only

Disciplines

1.2 COMPUTER AND INFORMATION SCIENCE, 1.4 CHEMICAL SCIENCES, 1.6 BIOLOGICAL SCIENCES

Publication Details

Ryan, B.J. and Barrett, R. (2007). ProteinParser--a community based tool for the generation of a detailed protein consensus and FASTA output. Computer Methods Programs Biomedicine, 85, (1), 69-76.

Abstract

Comparison of bioinformatic data is a common application in the life sciences and beyond. In this communication, a novel Java based software tool, ProteinParser, is outlined. This soft- ware tool calculates a detailed consensus, or most common, amino acid at a given position in an aligned protein set, whilst also generating a full consensus protein FASTA output. A second application of this software tool, computing a consensus amino acid given a toler- ance threshold, is also demonstrated. The phytase and the common bacterial 􏰀-lactamase proteins are analysed as ‘proof of concept’ examples. Consensus proteins, as generated by ProteinParser, are regularly utilised in the selection of residues for protein stabilisation muta- genesis; however, this widely applicable software tool will find many alternative applications in areas such as protein homology modelling.

DOI

10.1016/j.cmpb.2006.09.015

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Life Sciences Commons

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