PLUME (or "Promote economicaL, Useful and Maintained softwarE for the higher education and the research communities") is a repository of software for the research community (www.projet-plume.org).You can find the T-lex description in french here.
January 2012 - T-lex version 2 (T-lex2) |
T-lex2 is now available. Tlex2 returns much more accurate estimates of TE presence/absence using population NGS data compared to the original T-lex (see Manual pages). After the detection of ancestral genomic sequences, T-lex2 can reannotate individual TEs. T-lex2 also flags the putatively misannotated TE insertions.
We used T-lex2 and the DGRP data (Mackay et. al., 2012) to correct annotations for 108 TE insertions and to verify annotations for the rest (~1600) in the D. melanogaster reference genome. The reannotations and the reference genome sequence with and without TE sequences are available in the 'T-lex2 input data' page. These Tlex results will be also soon available via a dedicated database (see 'T-lex annotation').
April 2011 - T-lex version 1.1 |
Note that you can run T-lex (and other scripts) on a cloud using the Scalegenomics.com next-generation cloud service. We are in the process of creating the T-lex ScaleGenomics app so that you can run T-lex without any installation hassles.
Major changes between T-lex v0.1 and T-lex v1.1:
In the presence module, the sequence identity of the contig sequence overlapping the TE sequence is now taking into account to define the presence of a TE insertion. By default, the min sequence identity required for the presence is 70% (cf. help/ option '-id').
The identity, number of mismatches and matches are returned in the "Tresult" file.
