gff2aplot:: Plotting sequence comparisons

被引：5

作者：

Abril, JF

Guigó, R

Wiehe, T

机构：

[1] Univ Pompeu Fabra, Ctr Regulacio Gen, Inst Municipal Invest Med, Grp Rec Informat Biomed, Barcelona 08003, Spain

[2] Free Univ Berlin, D-14195 Berlin, Germany

来源：

BIOINFORMATICS | 2003年 / 19卷 / 18期

关键词：

D O I：

10.1093/bioinformatics/btg334

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

gff2aplot is a program to visualize the alignment of two sequences together with their annotations. Input for the program consists of single or multiple files in GFF-format which specify the alignment coordinates and annotation features of both sequences. Output is in PostScript format of any size. The features to be displayed are highly customizable to meet user specific needs. The program serves to generate print-quality images for comparative genome sequence analysis.

引用

页码：2477 / 2479

页数：3

共 16 条

[1] gff2ps:: visualizing genomic annotations [J].

Abril, JF ;

Guigó, R .

BIOINFORMATICS, 2000, 16 (08) :743-744

[2] The genome sequence of Drosophila melanogaster [J].

Adams, MD ;

Celniker, SE ;

Holt, RA ;

Evans, CA ;

Gocayne, JD ;

Amanatides, PG ;

Scherer, SE ;

Li, PW ;

Hoskins, RA ;

Galle, RF ;

George, RA ;

Lewis, SE ;

Richards, S ;

Ashburner, M ;

Henderson, SN ;

Sutton, GG ;

Wortman, JR ;

Yandell, MD ;

Zhang, Q ;

Chen, LX ;

Brandon, RC ;

Rogers, YHC ;

Blazej, RG ;

Champe, M ;

Pfeiffer, BD ;

Wan, KH ;

Doyle, C ;

Baxter, EG ;

Helt, G ;

Nelson, CR ;

Miklos, GLG ;

Abril, JF ;

Agbayani, A ;

An, HJ ;

Andrews-Pfannkoch, C ;

Baldwin, D ;

Ballew, RM ;

Basu, A ;

Baxendale, J ;

Bayraktaroglu, L ;

Beasley, EM ;

Beeson, KY ;

Benos, PV ;

Berman, BP ;

Bhandari, D ;

Bolshakov, S ;

Borkova, D ;

Botchan, MR ;

Bouck, J ;

Brokstein, P .

SCIENCE, 2000, 287 (5461) :2185-2195

[3] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].

Altschul, SF ;

Madden, TL ;

Schaffer, AA ;

Zhang, JH ;

Zhang, Z ;

Miller, W ;

Lipman, DJ .

NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402

[4] Alignment of whole genomes [J].

Delcher, AL ;

Kasif, S ;

Fleischmann, RD ;

Peterson, J ;

White, O ;

Salzberg, SL .

NUCLEIC ACIDS RESEARCH, 1999, 27 (11) :2369-2376

[5] The genome sequence of the malaria mosquito Anopheles gambiae [J].

Holt, RA ;

Subramanian, GM ;

Halpern, A ;

Sutton, GG ;

Charlab, R ;

Nusskern, DR ;

Wincker, P ;

Clark, AG ;

Ribeiro, JMC ;

Wides, R ;

Salzberg, SL ;

Loftus, B ;

Yandell, M ;

Majoros, WH ;

Rusch, DB ;

Lai, ZW ;

Kraft, CL ;

Abril, JF ;

Anthouard, V ;

Arensburger, P ;

Atkinson, PW ;

Baden, H ;

de Berardinis, V ;

Baldwin, D ;

Benes, V ;

Biedler, J ;

Blass, C ;

Bolanos, R ;

Boscus, D ;

Barnstead, M ;

Cai, S ;

Center, A ;

Chatuverdi, K ;

Christophides, GK ;

Chrystal, MA ;

Clamp, M ;

Cravchik, A ;

Curwen, V ;

Dana, A ;

Delcher, A ;

Dew, I ;

Evans, CA ;

Flanigan, M ;

Grundschober-Freimoser, A ;

Friedli, L ;

Gu, ZP ;

Guan, P ;

Guigo, R ;

Hillenmeyer, ME ;

Hladun, SL .

SCIENCE, 2002, 298 (5591) :129-+

[6] A TIME-EFFICIENT, LINEAR-SPACE LOCAL SIMILARITY ALGORITHM [J].

HUANG, XQ ;

MILLER, W .

ADVANCES IN APPLIED MATHEMATICS, 1991, 12 (03) :337-357

[7] Alfresco - A workbench for comparative genomic sequence analysis [J].

Jareborg, N ;

Durbin, R .

GENOME RESEARCH, 2000, 10 (08) :1148-1157

[8]

Kent WJ, 2002, GENOME RES, V12, P656, DOI [10.1101/gr.229202, 10.1101/gr.229202. Article published online before March 2002]

[9] VISTA:: visualizing global DNA sequence alignments of arbitrary length [J].

Mayor, C ;

Brudno, M ;

Schwartz, JR ;

Poliakov, A ;

Rubin, EM ;

Frazer, KA ;

Pachter, LS ;

Dubchak, I .

BIOINFORMATICS, 2000, 16 (11) :1046-1047

[10] Comparative gene prediction in human and mouse [J].

Parra, G ;

Agarwal, P ;

Abril, JF ;

Wiehe, T ;

Fickett, JW ;

Guigó, R .

GENOME RESEARCH, 2003, 13 (01) :108-117

← 1 2 →