CoSeg statistics

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Tool usage distribution map

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Associated diseases

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CoSeg specifications

Information


Unique identifier OMICS_25375
Name CoSeg
Software type Application/Script
Interface Command line interface
Restrictions to use None
Output data A tree data.
Output format GraphViz
Operating system Unix/Linux
Programming languages Perl
License Open Source License v2.1
Computer skills Advanced
Version 0.2.2
Stability Stable
Maintained Yes

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CoSeg in publications

 (7)
PMCID: 5858127
PMID: 29560044
DOI: 10.1186/s13100-018-0115-6

[…] set of alu elements was aligned to the aluy consensus sequence [] using cross_match (http://www.phrap.org/phredphrapconsed.html; last accessed december 2017). the data set was then analyzed via coseg (www.repeatmasker.org/cosegdownload.html; last accessed november 2017) to determine subfamilies. the middle a-rich region of the aluy consensus sequence was omitted while tri and di segregating […]

PMCID: 5640379
PMID: 29043294
DOI: 10.1126/sciadv.1701256

[…] and hence can be applied to re families of any genome., the first step toward understanding re activity is to identify the re subfamilies. a commonly used method for subfamily identification, coseg (), is based on multiple sequence alignments (msas) of a cohort of res being analyzed. a recent method, based on msas as well, goes on to infer the ancestry relations within a family of res […]

PMCID: 5622375
PMID: 28957461
DOI: 10.1093/gbe/evx172

[…] last accessed july 2016) with the following settings: -gap_init -25, gap_ext -5, -min score 200, -minmatch 6 –alignments –bandwidth 50 then analyzed via coseg (www.repeatmasker.org/cosegdownload.html; last accessed july 2016) to determine subfamily structure. the saimiri specific data set was aligned against the alus consensus sequence (). coseg […]

PMCID: 4432496
PMID: 25981446
DOI: 10.1186/s12864-015-1543-z

[…] a total of 119 hits corresponding to svas lacking the 5’ part of the sine-r were easily identifiable and analyzed separately. the remaining 1009 sequences were subjected to subfamily analysis using coseg [] with default settings., vntr analysis was performed for five to twenty elements per subfamily, depending on subfamily size. in case of the younger subfamilies svapa_7 to svapa_11 5’ […]

PMCID: 4436864
PMID: 25991928
DOI: 10.1186/s13100-015-0038-4

[…] 90% of the identified consensus were extracted, limiting ourselves to 15,000 hits from the genome drafts. the extracted sequences were combined into a single set of ves insertions and analyzed using coseg [,] after aligning them to the ves4_ml consensus sequence. a custom perl script provided by r. hubley was used to refine the consensus sequence for each ves subfamily and is available upon […]


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