Get 20M+ Full-Text Papers For Less Than $1.50/day. Start a 14-Day Trial for You or Your Team.

Learn More →

Integrated graphical analysis of protein sequence features predicted from sequence composition

Integrated graphical analysis of protein sequence features predicted from sequence composition Several protein sequence analysis algorithms are based on properties of amino acid composition and repetitiveness. These include methods for prediction of secondary structure elements, coiled‐coils, transmembrane segments or signal peptides, and for assignment of low‐complexity, nonglobular, or intrinsically unstructured regions. The quality of such analyses can be greatly enhanced by graphical software tools that present predicted sequence features together in context and allow judgment to be focused simultaneously on several different types of supporting information. For these purposes, we describe the SFINX package, which allows many different sets of segmental or continuous‐curve sequence feature data, generated by individual external programs, to be viewed in combination alongside a sequence dot‐plot or a multiple alignment of database matches. The implementation is currently based on extensions to the graphical viewers Dotter and Blixem and scripts that convert data from external programs to a simple generic data definition format called SFS. We describe applications in which dot‐plots and flanking database matches provide valuable contextual information for analyses based on compositional and repetitive sequence features. The system is also useful for comparing results from algorithms run with a range of parameters to determine appropriate values for defaults or cutoffs for large‐scale genomic analyses. Proteins 2001;45:262–273. © 2001 Wiley‐Liss, Inc. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Proteins: Structure Function and Bioinformatics Wiley

Integrated graphical analysis of protein sequence features predicted from sequence composition

Download PDF
12 pages

Loading next page...
 
/lp/wiley/integrated-graphical-analysis-of-protein-sequence-features-predicted-omKc9cVloy

References (37)

Publisher
Wiley
Copyright
Copyright © 2001 Wiley Subscription Services
ISSN
0887-3585
eISSN
1097-0134
DOI
10.1002/prot.1146
Publisher site
See Article on Publisher Site

Abstract

Several protein sequence analysis algorithms are based on properties of amino acid composition and repetitiveness. These include methods for prediction of secondary structure elements, coiled‐coils, transmembrane segments or signal peptides, and for assignment of low‐complexity, nonglobular, or intrinsically unstructured regions. The quality of such analyses can be greatly enhanced by graphical software tools that present predicted sequence features together in context and allow judgment to be focused simultaneously on several different types of supporting information. For these purposes, we describe the SFINX package, which allows many different sets of segmental or continuous‐curve sequence feature data, generated by individual external programs, to be viewed in combination alongside a sequence dot‐plot or a multiple alignment of database matches. The implementation is currently based on extensions to the graphical viewers Dotter and Blixem and scripts that convert data from external programs to a simple generic data definition format called SFS. We describe applications in which dot‐plots and flanking database matches provide valuable contextual information for analyses based on compositional and repetitive sequence features. The system is also useful for comparing results from algorithms run with a range of parameters to determine appropriate values for defaults or cutoffs for large‐scale genomic analyses. Proteins 2001;45:262–273. © 2001 Wiley‐Liss, Inc.

Journal

Proteins: Structure Function and Bioinformatics – Wiley

Published: Jan 15, 2001

Keywords: ; ; ; ; ; ; ; ; ; ;

There are no references for this article.