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Literature DB >> 15215346

The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences.

Michael Brudno¹, Rasmus Steinkamp, Burkhard Morgenstern.

Abstract

Cross-species sequence comparison is a powerful approach to analyze functional sites in genomic sequences and many discoveries have been made based on genomic alignments. Herein, we present a WWW-based software system for multiple alignment of large genomic sequences. Our server utilizes the previously developed combination of CHAOS and DIALIGN to achieve both speed and alignment accuracy. CHAOS is a fast database search tool that creates a list of local sequence similarities. These are used by DIALIGN as anchor points to speed up the final alignment procedure. The resulting alignment is returned to the user in different formats together with a list of anchor points found by CHAOS. The CHAOS/DIALIGN software is freely available at http://dialign.gobics.de/chaos-dialign-submission.

Mesh：

Year: 2004 PMID： 15215346 PMCID： PMC441499 DOI： 10.1093/nar/gkh361

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

17 in total

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Authors: B Morgenstern
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2. Analysis of vertebrate SCL loci identifies conserved enhancers.

Authors: B Göttgens; L M Barton; J G Gilbert; A J Bench; M J Sanchez; S Bahn; S Mistry; D Grafham; A McMurray; M Vaudin; E Amaya; D R Bentley; A R Green; A M Sinclair
Journal: Nat Biotechnol Date: 2000-02 Impact factor: 54.908

3. Exon discovery by genomic sequence alignment.

Authors: Burkhard Morgenstern; Oliver Rinner; Saïd Abdeddaïm; Dirk Haase; Klaus F X Mayer; Andreas W M Dress; Hans-Werner Mewes
Journal: Bioinformatics Date: 2002-06 Impact factor: 6.937

4. LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA.

Authors: Michael Brudno; Chuong B Do; Gregory M Cooper; Michael F Kim; Eugene Davydov; Eric D Green; Arend Sidow; Serafim Batzoglou
Journal: Genome Res Date: 2003-03-12 Impact factor: 9.043

5. AGenDA: homology-based gene prediction.

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Journal: Bioinformatics Date: 2003-08-12 Impact factor: 6.937

6. Surveying phylogenetic footprints in large gene clusters: applications to Hox cluster duplications.

Authors: Sonja J Prohaska; Claudia Fried; Christoph Flamm; Günter P Wagner; Peter F Stadler
Journal: Mol Phylogenet Evol Date: 2004-05 Impact factor: 4.286

7. Multiple DNA and protein sequence alignment based on segment-to-segment comparison.

Authors: B Morgenstern; A Dress; T Werner
Journal: Proc Natl Acad Sci U S A Date: 1996-10-29 Impact factor: 11.205

8. Independent Hox-cluster duplications in lampreys.

Authors: Claudia Fried; Sonja J Prohaska; Peter F Stadler
Journal: J Exp Zool B Mol Dev Evol Date: 2003-10-15 Impact factor: 2.656

9. Benchmarking tools for the alignment of functional noncoding DNA.

Authors: Daniel A Pollard; Casey M Bergman; Jens Stoye; Susan E Celniker; Michael B Eisen
Journal: BMC Bioinformatics Date: 2004-01-21 Impact factor: 3.169

10. Fast and sensitive multiple alignment of large genomic sequences.

Authors: Michael Brudno; Michael Chapman; Berthold Göttgens; Serafim Batzoglou; Burkhard Morgenstern
Journal: BMC Bioinformatics Date: 2003-12-23 Impact factor: 3.169

32 in total

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Authors: Xin Deng; Jianlin Cheng
Journal: BMC Bioinformatics Date: 2011-12-14 Impact factor: 3.169

2. DIALIGN: multiple DNA and protein sequence alignment at BiBiServ.

Authors: Burkhard Morgenstern
Journal: Nucleic Acids Res Date: 2004-07-01 Impact factor: 16.971

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Authors: Michael Freeling; Lakshmi Rapaka; Eric Lyons; Brent Pedersen; Brian C Thomas
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4. Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs.

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Journal: Genome Res Date: 2008-10-10 Impact factor: 9.043

5. ELAV-mediated 3'-end processing of ewg transcripts is evolutionarily conserved despite sequence degeneration of the ELAV-binding site.

Authors: Irmgard U Haussmann; Min Li; Matthias Soller
Journal: Genetics Date: 2011-07-29 Impact factor: 4.562

6. Augmentation of a wound response element accompanies the origin of a Hox-regulated Drosophila abdominal pigmentation trait.

Authors: Sumant Grover; Melissa E Williams; Rebecca Kaiser; Jesse T Hughes; Lauren Gresham; Mark Rebeiz; Thomas M Williams
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