Multiple whole genome alignments and novel biomedical applications at the VISTA portal

被引：22

作者：

Brudno, Michael ^{[2
]}

Poliakov, Alexander ^{[1
]}

Minovitsky, Simon ^{[1
]}

Ratnere, Igor ^{[1
]}

Dubchak, Inna ^{[1
,3
]}

机构：

[1] Univ Calif Berkeley, Lawrence Berkeley Lab, Genom Div, Berkeley, CA 94720 USA

[2] Univ Toronto, Dept Comp Sci, Banting & Best Dept Med Res, Toronto, ON M5S 3G4, Canada

[3] US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA

来源：

NUCLEIC ACIDS RESEARCH | 2007年 / 35卷

关键词：

D O I：

10.1093/nar/gkm279

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 [生物化学与分子生物学]; 081704 [应用化学];

摘要：

The VISTA portal for comparative genomics is designed to give biomedical scientists a unified set of tools to lead them from the raw DNA sequences through the alignment and annotation to the visualization of the results. The VISTA portal also hosts the alignments of a number of genomes computed by our group, allowing users to study the regions of their interest without having to manually download the individual sequences. Here we describe various algorithmic and functional improvements implemented in the VISTA portal over the last 2 years. The VISTA Portal is accessible at http://genome.lbl.gov/vista.

引用

页码：W669 / W674

页数：6

共 21 条

[1]

Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny [J].

Ahituv, N ;

Prabhakar, S ;

Rubin, EM ;

Couronne, O .

HUMAN MOLECULAR GENETICS, 2005, 14 (20) :3057-3063

[2]

Aligning multiple genomic sequences with the threaded blockset aligner [J].

Blanchette, M ;

Kent, WJ ;

Riemer, C ;

Elnitski, L ;

Smit, AFA ;

Roskin, KM ;

Baertsch, R ;

Rosenbloom, K ;

Clawson, H ;

Green, ED ;

Haussler, D ;

Miller, W .

GENOME RESEARCH, 2004, 14 (04) :708-715

[3]

MAVID: Constrained ancestral alignment of multiple sequences [J].

Bray, N ;

Pachter, L .

GENOME RESEARCH, 2004, 14 (04) :693-699

[4]

LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA [J].

Brudno, M ;

Do, CB ;

Cooper, GM ;

Kim, MF ;

Davydov, E ;

Green, ED ;

Sidow, A ;

Batzoglou, S .

GENOME RESEARCH, 2003, 13 (04) :721-731

[5]

Automated whole-genome multiple alignment of rat, mouse, and human [J].

Brudno, M ;

Poliakov, A ;

Salamov, A ;

Cooper, GM ;

Sidow, A ;

Rubin, EM ;

Solovyev, V ;

Batzoglou, S ;

Dubchak, I .

GENOME RESEARCH, 2004, 14 (04) :685-692

[6]

Glocal alignment: finding rearrangements during alignment [J].

Brudno, Michael ;

Malde, Sanket ;

Poliakov, Alexander ;

Do, Chuong B. ;

Couronne, Olivier ;

Dubchak, Inna ;

Batzoglou, Serafim .

BIOINFORMATICS, 2003, 19 :i54-i62

[7]

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

[8]

VISTA: computational tools for comparative genomics [J].

Frazer, KA ;

Pachter, L ;

Poliakov, A ;

Rubin, EM ;

Dubchak, I .

NUCLEIC ACIDS RESEARCH, 2004, 32 :W273-W279

[9]

TreeQ-VISTA: an interactive tree visualization tool with functional annotation query capabilities [J].

Gu, Shengyin ;

Anderson, Iain ;

Kunin, Victor ;

Cipriano, Michael ;

Minovitsky, Simon ;

Weber, Gunther ;

Amenta, Nina ;

Hamann, Bernd ;

Dubchak, Inna .

BIOINFORMATICS, 2007, 23 (06) :764-766

[10]

MATCH™:: a tool for searching transcription factor binding sites in DNA sequences [J].

Kel, AE ;

Gössling, E ;

Reuter, I ;

Cheremushkin, E ;

Kel-Margoulis, OV ;

Wingender, E .

NUCLEIC ACIDS RESEARCH, 2003, 31 (13) :3576-3579

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