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Protocols

CHAOS/DIALIGN specifications

Information


Unique identifier OMICS_29109
Name CHAOS/DIALIGN
Interface Web user interface
Restrictions to use None
Input data A single text file containing two or several genomic sequences.
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Burkhard Morgenstern

Publications for CHAOS/DIALIGN

CHAOS/DIALIGN citations

 (10)
library_books

Evidences for a New Role of miR 214 in Chondrogenesis

2018
Sci Rep
PMCID: 5829070
PMID: 29487295
DOI: 10.1038/s41598-018-21735-w

[…] mic sequences with 2.5 kilobase (Kb) were collected starting immediately upstream of pre-miR-199a-2 (now on called Dnm3os promoter). Multiple sequence alignment of Dnm3os promoter was performed using CHAOS/DIALIGN (http://dialign.gobics.de/chaos-dialign-submission) and fed to ConTra v2 (http://www.dmbr.ugent.be/prx/bioit2-public/contrav2/) for search of putative conserved TFBS. Stringency paramete […]

library_books

Redundant CArG Box Cis motif Activity Mediates SHATTERPROOF2 Transcriptional Regulation during Arabidopsis thaliana Gynoecium Development

2017
Front Plant Sci
PMCID: 5650620
PMID: 29085379
DOI: 10.3389/fpls.2017.01712

[…] tream regions (relative to the translation start site) of the SHP2 homologs in each of these species was obtained from Phytozome.net v10 () and was aligned using the multiple sequence aligner Dialign-Chaos (). Dialign-Chaos confers a score on each region of the alignment, with 9 denoting the highest level of sequence similarity and 0 the lowest. The output from the Dialign-Chaos alignment was conv […]

library_books

A comprehensive mapping of the structure and gene organisation in the sheep MHC class I region

2015
BMC Genomics
PMCID: 4613773
PMID: 26480943
DOI: 10.1186/s12864-015-1992-4

[…] quences were determined using the NCBI BLAST option to align two sequences (http://blast.ncbi.nlm.nih.gov/Blast.cgi). Sequences that overlapped at the 5′ or 3′ ends were subsequently aligned with the CHAOS/DIALIGN software [] provided at http://dialign.gobics.de/chaos-dialign-submission. Alignments were examined and edited, where required, using Seaview 4.2.12 [] to provide an optimal alignment an […]

library_books

Evolutionary divergence and limits of conserved non coding sequence detection in plant genomes

2011
Nucleic Acids Res
PMCID: 3152334
PMID: 21470961
DOI: 10.1093/nar/gkr179

[…] Alignment performance between different tools was conducted through comparing similarity scores resulting from BLASTN(), CHAOS (), DIALIGN () and LAGAN (), and comparisons revealed DIALIGN and BLASTN to perform best (, Supplementary Figures S3 and S4). The results of DIALIGN is comparable with those of BLASTN () and bet […]

library_books

A genome alignment algorithm based on compression

2010
BMC Bioinformatics
PMCID: 3022628
PMID: 21159205
DOI: 10.1186/1471-2105-11-599

[…] set, we applied each algorithm to align the mouse sequence against the human sequence, and compared the HSPs detected in the mouse sequence to the annotated mouse exons. The parameters for XMAligner, Chaos, Dialign, Nucmer and Blastz were the same as in the previous experiment. For Promer, we varied min cluster (c) and set minmatch (l) to 6 and maxgap to 30; for Sim4, we varied HSP threshold (C) a […]

call_split

Two Lamprey Hedgehog Genes Share Non Coding Regulatory Sequences and Expression Patterns with Gnathostome Hedgehogs

2010
PLoS One
PMCID: 2954159
PMID: 20967201
DOI: 10.1371/journal.pone.0013332
call_split See protocol

[…] quencing.Exons were predicted with BlastX searches and manual editing based on alignment with cDNA sequences and on the canonical splicing rules (see ). The nucleotide sequences were aligned with the CHAOS/DIALIGN program and the percent identities between the four identified Hhs were calculated using ClustalX (ver2.11) , . […]

Citations

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CHAOS/DIALIGN institution(s)
Department of Computer Science, Stanford University, Stanford, CA, USA; University of Gottingen, Institute of Microbiology and Genetics, Gottingen, Germany
CHAOS/DIALIGN funding source(s)
Supported by Deutsche Forschungsgemeinschaft, project MO 1048/1-1.

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