Dcode.org anthology of comparative genomic tools

被引：27

作者：

Loots, GG

Ovcharenko, I

机构：

[1] Lawrence Livermore Natl Lab, Genome Biol Div, Livermore, CA 94550 USA

[2] Lawrence Livermore Natl Lab, Energy Environm Biol & Inst Comp Dis, Livermore, CA 94550 USA

来源：

NUCLEIC ACIDS RESEARCH | 2005年 / 33卷

关键词：

D O I：

10.1093/nar/gki355

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：

Comparative genomics provides the means to demarcate functional regions in anonymous DNA sequences. The successful application of this method to identifying novel genes is currently shifting to deciphering the non-coding encryption of gene regulation across genomes. To facilitate the practical application of comparative sequence analysis to genetics and genomics, we have developed several analytical and visualization tools for the analysis of arbitrary sequences and whole genomes. These tools include two alignment tools, zPicture and Mulan; a phylogenetic shadowing tool, eShadow for identifying lineage- and species-specific functional elements; two evolutionary conserved transcription factor analysis tools, rVista and multiTF; a tool for extracting cis-regulatory modules governing the expression of co-regulated genes, Creme 2.0; and a dynamic portal to multiple vertebrate and invertebrate genome alignments, the ECR Browser. Here, we briefly describe each one of these tools and provide specific examples on their practical applications. All the tools are publicly available at the http://www.dcode.org/ website.

引用

页码：W56 / W64

页数：9

共 40 条

[1] Molecular screening of the TGIF gene in holoprosencephaly:: identification of two novel mutations [J].

Aguilella, C ;

Dubourg, C ;

Attia-Sobol, J ;

Vigneron, J ;

Blayau, M ;

Pasquier, L ;

Lazaro, L ;

Odent, S ;

David, V .

HUMAN GENETICS, 2003, 112 (02) :131-134

[2] HRC is a direct transcriptional target of MEF2 during cardiac, skeletal, and arterial smooth muscle development in vivo [J].

Anderson, JP ;

Dodou, E ;

Heidt, AB ;

De Val, SJ ;

Jaehnig, EJ ;

Greene, SB ;

Olson, EN ;

Black, BL .

MOLECULAR AND CELLULAR BIOLOGY, 2004, 24 (09) :3757-3768

[3] 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

[4] Intraspecies sequence comparisons for annotating genomes [J].

Boffelli, D ;

Weer, CV ;

Weng, L ;

Lewis, KD ;

Shoukry, MI ;

Pachter, L ;

Keys, DN ;

Rubin, EM .

GENOME RESEARCH, 2004, 14 (12) :2406-2411

[5] 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

[6] Functional characterization of transcription factor binding sites for HNF1-alpha, HNF3-beta (FOXA2), HNF4-alpha, Sp1 and Sp3 in the human prothrombin gene enhancer [J].

Ceelie, H ;

Spaargaren-Van Riel, CC ;

De Jong, M ;

Bertina, RM ;

Vos, HL .

JOURNAL OF THROMBOSIS AND HAEMOSTASIS, 2003, 1 (08) :1688-1698

[7] Positive autoregulation of the Myocyte enhancer factor-2 myogenic control gene during somatic muscle development in Drosophila [J].

Cripps, RM ;

Lovato, TL ;

Olson, EN .

DEVELOPMENTAL BIOLOGY, 2004, 267 (02) :536-547

[8] The ENCODE (ENCyclopedia of DNA elements) Project [J].

Feingold, EA ;

Good, PJ ;

Guyer, MS ;

Kamholz, S ;

Liefer, L ;

Wetterstrand, K ;

Collins, FS ;

Gingeras, TR ;

Kampa, D ;

Sekinger, EA ;

Cheng, J ;

Hirsch, H ;

Ghosh, S ;

Zhu, Z ;

Pate, S ;

Piccolboni, A ;

Yang, A ;

Tammana, H ;

Bekiranov, S ;

Kapranov, P ;

Harrison, R ;

Church, G ;

Struhl, K ;

Ren, B ;

Kim, TH ;

Barrera, LO ;

Qu, C ;

Van Calcar, S ;

Luna, R ;

Glass, CK ;

Rosenfeld, MG ;

Guigo, R ;

Antonarakis, SE ;

Birney, E ;

Brent, M ;

Pachter, L ;

Reymond, A ;

Dermitzakis, ET ;

Dewey, C ;

Keefe, D ;

Denoeud, F ;

Lagarde, J ;

Ashurst, J ;

Hubbard, T ;

Wesselink, JJ ;

Castelo, R ;

Eyras, E ;

Myers, RM ;

Sidow, A ;

Batzoglou, S .

SCIENCE, 2004, 306 (5696) :636-640

[9] Regulatory roles of conserved intergenic domains in vertebrate Dlx bigene clusters [J].

Ghanem, N ;

Jarinova, O ;

Amores, A ;

Long, QM ;

Hatch, G ;

Park, BK ;

Rubenstein, JLR ;

Ekker, M .

GENOME RESEARCH, 2003, 13 (04) :533-543

[10] GALA, a database for genomic sequence alignments and annotations [J].

Giardine, B ;

Elnitski, L ;

Riemer, C ;

Makalowska, L ;

Schwartz, S ;

Miller, W ;

Hardison, RC .

GENOME RESEARCH, 2003, 13 (04) :732-741

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