ProteinParser-A community based tool for the generation of a detailed protein consensus and FASTA output

Barry J. Ryan; Ronan Barrett

doi:10.1016/j.cmpb.2006.09.015

ProteinParser-A community based tool for the generation of a detailed protein consensus and FASTA output

Research output: Contribution to journal › Article › peer-review

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 software 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 tolerance threshold, is also demonstrated. The phytase and the common bacterial β-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 mutagenesis; however, this widely applicable software tool will find many alternative applications in areas such as protein homology modelling.

Original language	English
Pages (from-to)	69-76
Number of pages	8
Journal	Computer Methods and Programs in Biomedicine
Volume	85
Issue number	1
DOIs	https://doi.org/10.1016/j.cmpb.2006.09.015
Publication status	Published - Jan 2007
Externally published	Yes

Keywords

Amino acid frequency counting
Consensus concept
Protein alignment
Protein stabilisation

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10.1016/j.cmpb.2006.09.015

https://arrow.tudublin.ie/schfsehart/167Licence: CC BY-NC-SA

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ProteinParser-A community based tool for the generation of a detailed protein consensus and FASTA output

Abstract

Keywords

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