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Old 10-08-2012, 12:47 PM
satta
 
Default Bug#689961: ITP: ltrsift -- postprocessing and classification of LTR retrotransposons

Package: wnpp
Severity: wishlist
Owner: Sascha Steinbiss <steinbiss@zbh.uni-hamburg.de>

* Package name : ltrsift
Version : 1.0.1
Upstream Author : Sascha Steinbiss <steinbiss@zbh.uni-hamburg.de>
* URL : http://www.zbh.uni-hamburg.de/LTRsift
* License : GPL
Programming Lang: C
Description : postprocessing and classification of LTR retrotransposons

LTRsift is a graphical bioinformatics tool for semi-automatic postprocessing of de
novo predicted LTR retrotransposon annotations, such as the ones generated by
LTRharvest and LTRdigest (included in the genometools package).
Its user-friendly GTK interface displays LTR retrotransposon candidates,
their putative families and their internal structure in a hierarchical fashion,
allowing the user to "sift" through the sometimes large results of de novo
prediction software. It also offers customizable filtering and classification
functionality.

List of features:
* wizard-guided project creation and automated pre-classification
* "drag-and-drop' manual family assignment
* candidate filtering based on dynamic, customizable rule sets,
defined in a simple programming language (Lua)
* reference matching against custom FASTA files (BLAST required)
* ORF detection
* concise, customizable visualization of candidate structure
* candidate lists can be sorted by column values


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