FeatureStack: Perl module for comparative visualization of gene features

被引：6

作者：

Frech, Christian ^{[1
]}

Choo, Caleb ^{[1
]}

Chen, Nansheng ^{[1
]}

机构：

[1] Simon Fraser Univ, Dept Mol Biol & Biochem, Burnaby, BC V5A 1S6, Canada

来源：

BIOINFORMATICS | 2012年 / 28卷 / 23期

基金：

加拿大自然科学与工程研究理事会;

关键词：

EVOLUTION; GENOME;

D O I：

10.1093/bioinformatics/bts572

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

FeatureStack is a Perl module for the automatic generation of multi-gene images. FeatureStack takes BioPerl-compliant gene or transcript features as input and renders them side by side using a user-defined BioPerl glyph. Output images can be generated in SVG or PNG format. FeatureStack comes with a new BioPerl glyph, decorated_gene, which can highlight protein features on top of gene models. Used in combination, FeatureStack and decorated_gene enable rapid and automated generation of annotation-rich images of stacked gene models that greatly facilitate evolutionary studies of related gene structures and gene families.

引用

页码：3137 / 3138

页数：2

共 7 条

[1] Convergent evolution of RFX transcription factors and ciliary genes predated the origin of metazoans [J].

Chu, Jeffrey S. C. ;

Baillie, David L. ;

Chen, Nansheng .

BMC EVOLUTIONARY BIOLOGY, 2010, 10

[2] GECA: a fast tool for gene evolution and conservation analysis in eukaryotic protein families [J].

Fawal, Nizar ;

Savelli, Bruno ;

Dunand, Christophe ;

Mathe, Catherine .

BIOINFORMATICS, 2012, 28 (10) :1398-1399

[3]

Guo An-Yuan, 2007, Yichuan, V29, P1023, DOI 10.1360/yc-007-1023

[4] The genome of the simian and human malaria parasite Plasmodium knowlesi [J].

Pain, A. ;

Bohme, U. ;

Berry, A. E. ;

Mungall, K. ;

Finn, R. D. ;

Jackson, A. P. ;

Mourier, T. ;

Mistry, J. ;

Pasini, E. M. ;

Aslett, M. A. ;

Balasubrammaniam, S. ;

Borgwardt, K. ;

Brooks, K. ;

Carret, C. ;

Carver, T. J. ;

Cherevach, I. ;

Chillingworth, T. ;

Clark, T. G. ;

Galinski, M. R. ;

Hall, N. ;

Harper, D. ;

Harris, D. ;

Hauser, H. ;

Ivens, A. ;

Janssen, C. S. ;

Keane, T. ;

Larke, N. ;

Lapp, S. ;

Marti, M. ;

Moule, S. ;

Meyer, I. M. ;

Ormond, D. ;

Peters, N. ;

Sanders, M. ;

Sanders, S. ;

Sargeant, T. J. ;

Simmonds, M. ;

Smith, F. ;

Squares, R. ;

Thurston, S. ;

Tivey, A. R. ;

Walker, D. ;

White, B. ;

Zuiderwijk, E. ;

Churcher, C. ;

Quail, M. A. ;

Cowman, A. F. ;

Turner, C. M. R. ;

Rajandream, M. A. ;

Kocken, C. H. M. .

NATURE, 2008, 455 (7214) :799-U7

[5] FancyGene: dynamic visualization of gene structures and protein domain architectures on genomic loci [J].

Rambaldi, Davide ;

Ciccarelli, Francesca D. .

BIOINFORMATICS, 2009, 25 (17) :2281-2282

[6] The bioperl toolkit:: Perl modules for the life sciences [J].

Stajich, JE ;

Block, D ;

Boulez, K ;

Brenner, SE ;

Chervitz, SA ;

Dagdigian, C ;

Fuellen, G ;

Gilbert, JGR ;

Korf, I ;

Lapp, H ;

Lehväslaiho, H ;

Matsalla, C ;

Mungall, CJ ;

Osborne, BI ;

Pocock, MR ;

Schattner, P ;

Senger, M ;

Stein, LD ;

Stupka, E ;

Wilkinson, MD ;

Birney, E .

GENOME RESEARCH, 2002, 12 (10) :1611-1618

[7] The Generic Genome Browser: A building block for a model organism system database [J].

Stein, LD ;

Mungall, C ;

Shu, SQ ;

Caudy, M ;

Mangone, M ;

Day, A ;

Nickerson, E ;

Stajich, JE ;

Harris, TW ;

Arva, A ;

Lewis, S .

GENOME RESEARCH, 2002, 12 (10) :1599-1610

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