ColinearScan statistics

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ColinearScan specifications

Information


Unique identifier OMICS_11728
Name ColinearScan
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Genetic markers such as sequences
Operating system Unix/Linux
Programming languages C++, Perl
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.0.1
Stability Stable
Requirements
BioPerl, Getopt::Long, Pod::Usage
Maintained Yes

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  • person_outline ColinearScan <>

Publication for ColinearScan

ColinearScan in publications

 (9)
PMCID: 5850751
PMID: 29029269
DOI: 10.1093/molbev/msx242

[…] nodes., gene colinearity, reflecting shared ancestral gene order, is crucial to understand the genomic changes, especially in deconvoluting the evolution of complex plant genomes. by using colinearscan, we detected colinear genes within each cucurbit genome and between each pair of them (, online). grape genome was used as an outgroup reference to decipher the cucurbit genomes. […]

PMCID: 5388744
PMID: 28446920
DOI: 10.3389/fpls.2017.00571

[…] respectively, to help distinguish homologies related to different events, recursive polyploidizations, and speciation., with the information on putative homologous genes as the input, we ran a colinearscan () to infer colinear relationships that would reveal homologous blocks within each genome and between genomes. synonymous nucleotide substitutions per synonymous site (ks) […]

PMCID: 5047885
PMID: 27757123
DOI: 10.3389/fgene.2016.00174

[…] by running blastp among genes, we searched for potential anchors (e-value ≤ 1e-5; top five matches) between every possible pair of chromosomes within rice and pineapple, and between them. by running colinearscan (), we revealed homologous blocks within each genome and between different genomes (by setting maximal searching gap ≤ 50 genes and p-value < 0.05). by characterizing homologous […]

PMCID: 4595991
PMID: 26504573
DOI: 10.1038/hortres.2015.26

[…] search for potential anchors (e < 1e−10, top 5 matches) in the c. x clementina genome. afterwards, mcscan was employed to identify homologous regions. finally, syntenic blocks were evaluated by colinearscan. alignments with an e value < 1e−10 were considered as significant matches. the expression data of 371 c. sinensis genes were downloaded from cap and the correlation coefficients […]

PMCID: 4072886
PMID: 24906560
DOI: 10.1186/1471-2164-15-444

[…] local server. then mcscan (multiple collinearity scan) [] was used to obtain the collinearity relation of each pair of species. the resulting collinearity chains were evaluated using a procedure in colinearscan and an e-value < 1e-10 was used as the cutoff., to examine the expression of pear genes, pear (pyrus bretschneideri) fruit samples at 15 d, 36 d, 80 d, 110 d, 145 d and 167 d […]


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ColinearScan institution(s)
College of Life Sciences, National Laboratory of Plant Genetic Engineering and Protein Engineering, Center of Bioinformatics, Peking University, Beijing, China; College of Mathematics, Hebei Polytechnic University, Tangshan, Hebei, China; Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China; Beijing Genomics Institute, Chinese Academy of Sciences, Beijing, China
ColinearScan funding source(s)
This study was supported by the National Key Basic Research Program of China (973 No 2003CB715900), Natural Science Foundation of China (NSFC, No 90408015 and 30170232) and the China High-tech Program, the China High Technology Platform and the Program of Introducing Talents of Discipline to Universities, no. B06001.

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