GenomeDiagram: a python']python package for the visualization of large-scale genomic data

被引：69

作者：

Pritchard, L ^{[1
]}

White, JA ^{[1
]}

Birch, PRJ ^{[1
]}

Toth, IK ^{[1
]}

机构：

[1] Scottish Crop Res Inst, Plant Pathogen Programme, Dundee DD2 5DA, Scotland

来源：

BIOINFORMATICS | 2006年 / 22卷 / 05期

关键词：

D O I：

10.1093/bioinformatics/btk021

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

We present GenomeDiagram, a flexible, open-source Python module for the visualization of large-scale genomic, comparative genomic and other data with reference to a single chromosome or other biological sequence. GenomeDiagram may be used to generate publication-quality vector graphics, rastered images and in-line streamed graphics for webpages. The package integrates with datatypes from the BioPython project, and is available for Windows, Linux and Mac OS X systems. Availability: GenomeDiagram is freely available as source code (under GNU Public License) at http://bioinf.scri.ac.uk/lp/programs.html, and requires Python 2.3 or higher, and recent versions of the ReportLab and BioPython packages. Contact: lpritc@scri.ac.uk Supplementary Information A user manual, example code and images are available at http://bioinf.scri.ac.uk/lp/programs.html.

引用

页码：616 / 617

页数：2

共 8 条

[1] WebACT - an online companion for the artemis comparison tool [J].

Abbott, JC ;

Aanensen, DM ;

Rutherford, K ;

Butcher, S ;

Spratt, BG .

BIOINFORMATICS, 2005, 21 (18) :3665-3666

[2] Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp atroseptica and characterization of virulence factors [J].

Bell, KS ;

Sebaihia, M ;

Pritchard, L ;

Holden, MTG ;

Hyman, LJ ;

Holeva, MC ;

Thomson, NR ;

Bentley, SD ;

Churcher, LJC ;

Mungall, K ;

Atkin, R ;

Bason, N ;

Brooks, K ;

Chillingworth, T ;

Clark, K ;

Doggett, J ;

Fraser, A ;

Hance, Z ;

Hauser, H ;

Jagels, K ;

Moule, S ;

Norbertczak, H ;

Ormond, D ;

Price, C ;

Quail, MA ;

Sanders, M ;

Walker, D ;

Whitehead, S ;

Salmond, GPC ;

Birch, PRJ ;

Parkhill, J ;

Toth, IK .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2004, 101 (30) :11105-11110

[3] ACT: the Artemis comparison tool [J].

Carver, TJ ;

Rutherford, KM ;

Berriman, M ;

Rajandream, MA ;

Barrell, BG ;

Parkhill, J .

BIOINFORMATICS, 2005, 21 (16) :3422-3423

[4] Mauve: Multiple alignment of conserved genomic sequence with rearrangements [J].

Darling, ACE ;

Mau, B ;

Blattner, FR ;

Perna, NT .

GENOME RESEARCH, 2004, 14 (07) :1394-1403

[5] EnteriX 2003: visualization tools for genome alignments of Enterobacteriaceae [J].

Florea, L ;

McClelland, M ;

Riemer, C ;

Schwartz, S ;

Miller, W .

NUCLEIC ACIDS RESEARCH, 2003, 31 (13) :3527-3532

[6] GenomeViz: visualizing microbial genomes [J].

Ghai, R ;

Hain, T ;

Chakraborty, T .

BMC BIOINFORMATICS, 2004, 5 (1)

[7] Three views of microbial genomes [J].

Jensen, LJ ;

Friis, C ;

Ussery, DW .

RESEARCH IN MICROBIOLOGY, 1999, 150 (9-10) :773-777

[8] Visualization for genomics: The microbial genome viewer [J].

Kerkhoven, R ;

van Enckevort, FHJ ;

Boekhorst, J ;

Molenaar, D ;

Siezen, RJ .

BIOINFORMATICS, 2004, 20 (11) :1812-1814

← 1 →