LTRsift

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

 

 

To ease manual curation it also supports GUI-driven reassignment, splitting and further annotation of candidates. Export of grouped candidate sets is possible in  standard formats (GFF3 for annotations, FASTA for sequences).

Features

Availability

LTRsift can be downloaded here for 64-bit Intel Linux and Mac OS X platforms.

The source code (GPL) is available from a Git repository at http://github.com/satta/ltrsift.
Note that some external libraries, e.g. Cairo and GTK+, are required. Read more about these dependencies.

LTRsift is also currently available in the Debian unstable and Ubuntu package repositories (packages ltrsift and ltrsift-examples) as part of Debian Med.

Bug reports and wishlist

Have you encountered something that you feel may be a bug in LTRsift or do you have a suggestion for improvement? Just file a ticket in our on-line issue tracker!

Example Data

We offer input GFF3 candidate annotations from the paper (from LTRharvest/LTRdigest) and the corresponding sequences in FASTA format for download as gzipped tar archives:

Developers

LTRsift has been developed by Sascha Kastens and Sascha Steinbiss, with parts of the software written by Joachim Bonnet.

Contact

Sascha Steinbiss
Center for Bioinformatics, University of Hamburg
Bundesstr. 43, 20146 Hamburg, Germany
Phone +49 40 42838 7322, Fax. +49 40 42838 7312