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PR2ALIGN: a stand-alone software program and a web-server for protein sequence alignment using weighted biochemical properties of amino acids.

Kuznetsov IB, McDuffie M - BMC Res Notes (2015)

Bottom Line: Moreover, most existing amino acid substitution matrices account for the average (dis)similarities between amino acid types and do not distinguish the contribution of a specific biochemical property to these (dis)similarities.We show that in many cases the approach implemented in PR2ALIGN produces better quality pair-wise alignments than the conventional matrix-based approach.To the best of the authors' knowledge, there are no existing stand-alone software programs or web-servers analogous to PR2ALIGN.

View Article: PubMed Central - PubMed

Affiliation: Cancer Research Center and Department of Epidemiology and Biostatistics, University at Albany, State University of New York, One Discovery Drive, Rensselaer, NY, 12144, USA. ikuznetsov@albany.edu.

ABSTRACT

Background: Alignment of amino acid sequences is the main sequence comparison method used in computational molecular biology. The selection of the amino acid substitution matrix best suitable for a given alignment problem is one of the most important decisions the user has to make. In a conventional amino acid substitution matrix all elements are fixed and their values cannot be easily adjusted. Moreover, most existing amino acid substitution matrices account for the average (dis)similarities between amino acid types and do not distinguish the contribution of a specific biochemical property to these (dis)similarities.

Findings: PR2ALIGN is a stand-alone software program and a web-server that provide the functionality for implementing flexible user-specified alignment scoring functions and aligning pairs of amino acid sequences based on the comparison of the profiles of biochemical properties of these sequences. Unlike the conventional sequence alignment methods that use 20x20 fixed amino acid substitution matrices, PR2ALIGN uses a set of weighted biochemical properties of amino acids to measure the distance between pairs of aligned residues and to find an optimal minimal distance global alignment. The user can provide any number of amino acid properties and specify a weight for each property. The higher the weight for a given property, the more this property affects the final alignment. We show that in many cases the approach implemented in PR2ALIGN produces better quality pair-wise alignments than the conventional matrix-based approach.

Conclusions: PR2ALIGN will be helpful for researchers who wish to align amino acid sequences by using flexible user-specified alignment scoring functions based on the biochemical properties of amino acids instead of the amino acid substitution matrix. To the best of the authors' knowledge, there are no existing stand-alone software programs or web-servers analogous to PR2ALIGN. The software is freely available from http://pr2align.rit.albany.edu.

No MeSH data available.


The input page of the web-server implementation of PR2ALIGN.
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Related In: Results  -  Collection

License 1 - License 2
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Fig2: The input page of the web-server implementation of PR2ALIGN.

Mentions: The alignment program was also implemented as a freely available web-server (http://pr2align.rit.albany.edu). The web-server has a simple user interface (FigureĀ 2) that consists of the four input fields described below. Instructions for each field and general information about the method and the output format can be found in the help pages.Figure 2


PR2ALIGN: a stand-alone software program and a web-server for protein sequence alignment using weighted biochemical properties of amino acids.

Kuznetsov IB, McDuffie M - BMC Res Notes (2015)

The input page of the web-server implementation of PR2ALIGN.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4477417&req=5

Fig2: The input page of the web-server implementation of PR2ALIGN.
Mentions: The alignment program was also implemented as a freely available web-server (http://pr2align.rit.albany.edu). The web-server has a simple user interface (FigureĀ 2) that consists of the four input fields described below. Instructions for each field and general information about the method and the output format can be found in the help pages.Figure 2

Bottom Line: Moreover, most existing amino acid substitution matrices account for the average (dis)similarities between amino acid types and do not distinguish the contribution of a specific biochemical property to these (dis)similarities.We show that in many cases the approach implemented in PR2ALIGN produces better quality pair-wise alignments than the conventional matrix-based approach.To the best of the authors' knowledge, there are no existing stand-alone software programs or web-servers analogous to PR2ALIGN.

View Article: PubMed Central - PubMed

Affiliation: Cancer Research Center and Department of Epidemiology and Biostatistics, University at Albany, State University of New York, One Discovery Drive, Rensselaer, NY, 12144, USA. ikuznetsov@albany.edu.

ABSTRACT

Background: Alignment of amino acid sequences is the main sequence comparison method used in computational molecular biology. The selection of the amino acid substitution matrix best suitable for a given alignment problem is one of the most important decisions the user has to make. In a conventional amino acid substitution matrix all elements are fixed and their values cannot be easily adjusted. Moreover, most existing amino acid substitution matrices account for the average (dis)similarities between amino acid types and do not distinguish the contribution of a specific biochemical property to these (dis)similarities.

Findings: PR2ALIGN is a stand-alone software program and a web-server that provide the functionality for implementing flexible user-specified alignment scoring functions and aligning pairs of amino acid sequences based on the comparison of the profiles of biochemical properties of these sequences. Unlike the conventional sequence alignment methods that use 20x20 fixed amino acid substitution matrices, PR2ALIGN uses a set of weighted biochemical properties of amino acids to measure the distance between pairs of aligned residues and to find an optimal minimal distance global alignment. The user can provide any number of amino acid properties and specify a weight for each property. The higher the weight for a given property, the more this property affects the final alignment. We show that in many cases the approach implemented in PR2ALIGN produces better quality pair-wise alignments than the conventional matrix-based approach.

Conclusions: PR2ALIGN will be helpful for researchers who wish to align amino acid sequences by using flexible user-specified alignment scoring functions based on the biochemical properties of amino acids instead of the amino acid substitution matrix. To the best of the authors' knowledge, there are no existing stand-alone software programs or web-servers analogous to PR2ALIGN. The software is freely available from http://pr2align.rit.albany.edu.

No MeSH data available.