ProfileGrids: a sequence alignment visualization paradigm that avoids the limitations of Sequence Logos

BMC Proceedings

Research

Alberto I Roca¹ 

[1] ProfileGrid.org, P.O. Box 6414, 92616, Irvine, California, USA;

关键词: Multiple Sequence Alignment;    Sequence Logo;    Protein Multiple Sequence Alignment;    Residue Symbol;    Residue Frequency;   

DOI  :  10.1186/1753-6561-8-S2-S6

来源: Springer

【 摘 要 】

BackgroundThe 2013 BioVis Contest provided an opportunity to evaluate different paradigms for visualizing protein multiple sequence alignments. Such data sets are becoming extremely large and thus taxing current visualization paradigms. Sequence Logos represent consensus sequences but have limitations for protein alignments. As an alternative, ProfileGrids are a new protein sequence alignment visualization paradigm that represents an alignment as a color-coded matrix of the residue frequency occurring at every homologous position in the aligned protein family.ResultsThe JProfileGrid software program was used to analyze the BioVis contest data sets to generate figures for comparison with the Sequence Logo reference images.ConclusionsThe ProfileGrid representation allows for the clear and effective analysis of protein multiple sequence alignments. This includes both a general overview of the conservation and diversity sequence patterns as well as the interactive ability to query the details of the protein residue distributions in the alignment. The JProfileGrid software is free and available from http://www.ProfileGrid.org.

【 授权许可】

CC BY   
© Roca; licensee BioMed Central Ltd. 2014