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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

Versioning


No version available

CoSeg citations

 (6)
library_books

Analysis of lineage specific Alu subfamilies in the genome of the olive baboon, Papio anubis

2018
Mob DNA
PMCID: 5858127
PMID: 29560044
DOI: 10.1186/s13100-018-0115-6

[…] e is more resolved and displays a defined branching pattern between all subfamilies. The Bayesian tree also displays subfamily relationships that are highly similar to the relationships determined by COSEG displayed in Fig. . Based on the Bayesian tree and alignments, we were able to determine the relative radiation of our Alu subfamilies and their possible derivatives.Fig. 4 […]

library_books

Integrating networks and comparative genomics reveals retroelement proliferation dynamics in hominid genomes

2017
Sci Adv
PMCID: 5640379
PMID: 29043294
DOI: 10.1126/sciadv.1701256

[…] d generic 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 usin […]

library_books

Evolution of Alu Subfamily Structure in the Saimiri Lineage of New World Monkeys

2017
Genome Biol Evol
PMCID: 5622375
PMID: 28957461
DOI: 10.1093/gbe/evx172

[…] rmat in , online. To further investigate subfamily structure of the Saimiri lineage, a custom RepeatMasker library was created and the data set was RepeatMasked against the subfamilies identified by COSEG, the subfamilies identified in the Marmoset Consortium project and the Alu Consensus sequences from the RepeatMasker library. This was done to ensure sequences were as closely (matched) identifi […]

call_split

Differential SINE evolution in vesper and non vesper bats

2015
Mob DNA
PMCID: 4436864
PMID: 25991928
DOI: 10.1186/s13100-015-0038-4
call_split See protocol

[…] 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 reque […]

library_books

Inference of Transposable Element Ancestry

2014
PLoS Genet
PMCID: 4133154
PMID: 25121584
DOI: 10.1371/journal.pgen.1004482

[…] We have confirmed here that the CoSeg subfamily classification method fails to identify many highly-probable ancestral sequences in both LAVA and AluSc, and therefore that CoSeg subfamily consensus sequences are problematic for use as presumed ancestors in divergence and substitution analysis. In contrast, the AnTE method we developed and describe here provides a detail […]

library_books

Reviving the Dead: History and Reactivation of an Extinct L1

2014
PLoS Genet
PMCID: 4072516
PMID: 24968166
DOI: 10.1371/journal.pgen.1004395

[…] ences with >60% identity and >90% coverage of the query. Using 2000 random sequences from the CENSOR run, subfamilies were identified based on shared sequence variants (co-segregating mutations) with COSEG 0.2.1 (http://www.repeatmasker.org/COSEGDownload.html) following the default parameters. Nine subfamilies were generated and their consensuses used as query sequences for a second round of CENS […]

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