Visualization of multiple genome annotations and alignments with the K-BROWSER

被引：11

作者：

Chakrabarti, K

Pachter, L ^{[1
]}

机构：

[1] Univ Calif Berkeley, Dept Math, Berkeley, CA 94720 USA

[2] Univ Calif Berkeley, Dept Comp Sci, Berkeley, CA 94720 USA

来源：

GENOME RESEARCH | 2004年 / 14卷 / 04期

关键词：

D O I：

10.1101/gr.1957004

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

We introduce a novel genome browser application, the K-BROWSER, that allows intuitive visualization of biological information across an arbitrary number of multiply aligned genomes. In particular, the K-BROWSER simultaneously displays an arbitrary number of genomes both through overlaid annotations and predictions that describe their respective characteristics, and through the multiple alignment that describes their global relationship to one another. The browsing environment has been designed to allow users seamless access to information available in every genome and, furthermore, to allow easy navigation within and between genomes. As of the date of publication, the K-BROWSER has been set up on the human, mouse, and rat genomes.

引用

页码：716 / 720

页数：5

共 15 条

[1] SLAM: Cross-species gene finding and alignment with a generalized pair hidden Markov model [J].

Alexandersson, M ;

Cawley, S ;

Pachter, L .

GENOME RESEARCH, 2003, 13 (03) :496-502

[2] Phylogenetic shadowing of primate sequences to find functional regions of the human genome [J].

Boffelli, D ;

McAuliffe, J ;

Ovcharenko, D ;

Lewis, KD ;

Ovcharenko, I ;

Pachter, L ;

Rubin, EM .

SCIENCE, 2003, 299 (5611) :1391-1394

[3] AVID: A global alignment program [J].

Bray, N ;

Dubchak, I ;

Pachter, L .

GENOME RESEARCH, 2003, 13 (01) :97-102

[4] Ensembl 2002: accommodating comparative genomics [J].

Clamp, M ;

Andrews, D ;

Barker, D ;

Bevan, P ;

Cameron, G ;

Chen, Y ;

Clark, L ;

Cox, T ;

Cuff, J ;

Curwen, V ;

Down, T ;

Durbin, R ;

Eyras, E ;

Gilbert, J ;

Hammond, M ;

Hubbard, T ;

Kasprzyk, A ;

Keefe, D ;

Lehvaslaiho, H ;

Iyer, V ;

Melsopp, C ;

Mongin, E ;

Pettett, R ;

Potter, S ;

Rust, A ;

Schmidt, E ;

Searle, S ;

Slater, G ;

Smith, J ;

Spooner, W ;

Stabenau, A ;

Stalker, J ;

Stupka, E ;

Ureta-Vidal, A ;

Vastrik, I ;

Birney, E .

NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :38-42

[5] Finding functional features in Saccharomyces genomes by phylogenetic footprinting [J].

Cliften, P ;

Sudarsanam, P ;

Desikan, A ;

Fulton, L ;

Fulton, B ;

Majors, J ;

Waterston, R ;

Cohen, BA ;

Johnston, M .

SCIENCE, 2003, 301 (5629) :71-76

[6] Strategies and tools for whole-genome alignments [J].

Couronne, O ;

Poliakov, A ;

Bray, N ;

Ishkhanov, T ;

Ryaboy, D ;

Rubin, E ;

Pachter, L ;

Dubchak, I .

GENOME RESEARCH, 2003, 13 (01) :73-80

[7] The Ensembl genome database project [J].

Hubbard, T ;

Barker, D ;

Birney, E ;

Cameron, G ;

Chen, Y ;

Clark, L ;

Cox, T ;

Cuff, J ;

Curwen, V ;

Down, T ;

Durbin, R ;

Eyras, E ;

Gilbert, J ;

Hammond, M ;

Huminiecki, L ;

Kasprzyk, A ;

Lehvaslaiho, H ;

Lijnzaad, P ;

Melsopp, C ;

Mongin, E ;

Pettett, R ;

Pocock, M ;

Potter, S ;

Rust, A ;

Schmidt, E ;

Searle, S ;

Slater, G ;

Smith, J ;

Spooner, W ;

Stabenau, A ;

Stalker, J ;

Stupka, E ;

Ureta-Vidal, A ;

Vastrik, I ;

Clamp, M .

NUCLEIC ACIDS RESEARCH, 2002, 30 (01) :38-41

[8] The UCSC Genome Browser Database [J].

Karolchik, D ;

Baertsch, R ;

Diekhans, M ;

Furey, TS ;

Hinrichs, A ;

Lu, YT ;

Roskin, KM ;

Schwartz, M ;

Sugnet, CW ;

Thomas, DJ ;

Weber, RJ ;

Haussler, D ;

Kent, WJ .

NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :51-54

[9] Sequencing and comparison of yeast species to identify genes and regulatory elements [J].

Kellis, M ;

Patterson, N ;

Endrizzi, M ;

Birren, B ;

Lander, ES .

NATURE, 2003, 423 (6937) :241-254

[10] The human genome browser at UCSC [J].

Kent, WJ ;

Sugnet, CW ;

Furey, TS ;

Roskin, KM ;

Pringle, TH ;

Zahler, AM ;

Haussler, D .

GENOME RESEARCH, 2002, 12 (06) :996-1006

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