Combo: a whole genome comparative browser

被引:30
作者
Engels, Reinhard
Yu, Tamara
Burge, Chris
Mesirov, Jill P.
DeCaprio, David
Galagan, James E.
机构
[1] MIT, Broad Inst, Cambridge, MA 02142 USA
[2] Harvard Univ, Cambridge, MA 02142 USA
[3] MIT, Dept Biol, Cambridge, MA 02139 USA
关键词
D O I
10.1093/bioinformatics/btl193
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Combo is a comparative genome browser that provides a dynamic view of whole genome alignments along with their associated annotations. Combo provides two different visualization perspectives. The perpendicular (dot plot) view provides a dot plot of genome alignments synchronized with a display of genome annotations along each axis. The parallel view displays two genome annotations horizontally, synchronized through a panel displaying local alignments as trapezoids. Users can zoom to any resolution, from whole chromosomes to individual bases. They can select, highlight and view detailed information from specific alignments and annotations. Combo is an organism agnostic and can import data from a variety of file formats.
引用
收藏
页码:1782 / 1783
页数:2
相关论文
共 9 条
[1]   gff2aplot:: Plotting sequence comparisons [J].
Abril, JF ;
Guigó, R ;
Wiehe, T .
BIOINFORMATICS, 2003, 19 (18) :2477-2479
[2]   BASIC LOCAL ALIGNMENT SEARCH TOOL [J].
ALTSCHUL, SF ;
GISH, W ;
MILLER, W ;
MYERS, EW ;
LIPMAN, DJ .
JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410
[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]   Ensembl 2005 [J].
Hubbard, T ;
Andrews, D ;
Caccamo, M ;
Cameron, G ;
Chen, Y ;
Clamp, M ;
Clarke, L ;
Coates, G ;
Cox, T ;
Cunningham, F ;
Curwen, V ;
Cutts, T ;
Down, T ;
Durbin, R ;
Fernandez-Suarez, XM ;
Gilbert, J ;
Hammond, M ;
Herrero, J ;
Hotz, H ;
Howe, K ;
Iyer, V ;
Jekosch, K ;
Kahari, A ;
Kasprzyk, A ;
Keefe, D ;
Keenan, S ;
Kokocinsci, F ;
London, D ;
Longden, I ;
McVicker, G ;
Melsopp, C ;
Meidl, P ;
Potter, S ;
Proctor, G ;
Rae, M ;
Rios, D ;
Schuster, M ;
Searle, S ;
Severin, J ;
Slater, G ;
Smedley, D ;
Smith, J ;
Spooner, W ;
Stabenau, A ;
Stalker, J ;
Storey, R ;
Trevanion, S ;
Ureta-Vidal, A ;
Vogel, J ;
White, S .
NUCLEIC ACIDS RESEARCH, 2005, 33 :D447-D453
[5]  
Lewis SE., 2002, Genome Biol, V3, DOI DOI 10.1186/GB-2002-3-12-RESEARCH0082
[6]  
Li Ming, 2003, Genome Inform, V14, P164
[7]  
Li Ming, 2004, J Bioinform Comput Biol, V2, P417, DOI 10.1142/S0219720004000661
[8]   PatternHunter: faster and more sensitive homology search [J].
Ma, B ;
Tromp, J ;
Li, M .
BIOINFORMATICS, 2002, 18 (03) :440-445
[9]   A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis (Reprinted from Gene Combis, vol 167, pg GC1-GC10, 1996) [J].
Sonnhammer, ELL ;
Durbin, R .
GENE, 1995, 167 (1-2) :GC1-GC10