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REannotate specifications

Information


Unique identifier OMICS_18079
Name REannotate
Alternative name Repetitive Element re-annotation
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTA
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 3.0
Computer skills Advanced
Version 26.11.2007
Stability Stable
Source code URL http://www.bioinformatics.org/reannotate/download/REannotate
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Vini Pereira

Publication for Repetitive Element re-annotation

REannotate citations

 (4)
call_split

Phylogenetic Analysis Reveals That ERVs 'Die Young' but HERV H Is Unusually Conserved

2016
PLoS Comput Biol
PMCID: 4905674
PMID: 27295277
DOI: 10.1371/journal.pcbi.1004964
call_split See protocol

[…] e repeats identified by RepeatMasker are often fragmented so that an LTR element originating from a single insertion event is referenced using several distinct annotations. For this reason we applied REannotate 26.11.2007 [] using options -c -n -f to our RepeatMasker results. This resulted in the identification of complete ERVs, truncated ERVs, and solo-LTRs, entities corresponding to distinct ins […]

library_books

A novel reannotation strategy for dissecting DNA methylation patterns of human long intergenic non coding RNAs in cancers

2014
Nucleic Acids Res
PMCID: 4117791
PMID: 25013169
DOI: 10.1093/nar/gku575

[…] of six cell lines were from Gene Expression Omnibus (GEO, GSE23316) (). Corresponding lincRNA expression data from patients were calculated based on the RNA-seq V2 data from TCGA. CGI annotation and repetitive element (RE) annotation data were from UCSC Genome Browser (). Annotation files for lincRNAs and protein-coding genes (PCGs) were downloaded from Human lincRNA Catalog (). […]

call_split

Evolutionary Genomics of Transposable Elements in Saccharomyces cerevisiae

2012
PLoS One
PMCID: 3511429
PMID: 23226439
DOI: 10.1371/journal.pone.0050978
call_split See protocol

[…] reliminary analyses that revealed additional Ty3-like sequences in the S. cerevisiae genome that were not fully identified using the Ty3 element as a query.RepeatMasker output was then processed with REannotate version 26.11.2007 (options: -g -f -d 10000) in order to join LTRs to internal sequences and defragment nested and degenerate insertions (see for an example screenshot of the REannotate o […]

call_split

The Effect of Transposable Element Insertions on Gene Expression Evolution in Rodents

2009
PLoS One
PMCID: 2629548
PMID: 19183808
DOI: 10.1371/journal.pone.0004321
call_split See protocol

[…] p the homology between the consensus and the TE sequence. And third, TEs sometimes insert into other TEs breaking them into two parts. We therefore applied a new algorithm, implemented in the program ReAnnotate , to join these disparate parts into single TE elements where possible, a process we call defragmentation. In short the algorithm connects TE fragments to each other that are in the same or […]

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REannotate institution(s)
Department of Life Sciences, Imperial College London, Silwood Park campus, Ascot, Berkshire, UK; Theoretical Systems Biology, Institute of Food Research, Norwich Research Park, Colney, Norwich, UK

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