Transposable Element Annotation

DAWGPAWS includes scripts to work with computational evidences from the following standalone programs and web services for transposable element annotation. You can get information for the following programs by clicking on the annotation program name, and you can get the documentation for the DAWGPAWS script by clicking on the script name. For full information on installing and using these programs, see the DAWGPAWS manual.

The individual annotation programs are not included in the DAWGPAWS package and must be installed separately.

Program
DAWGPAWS Script
LTR_STRUC
ltrstruc_prep.pl
batch_ltrstruc.vbs
cnv_ltrstruc2gff.pl
LTR_Finder batch_ltrfinder.pl
cnv_ltrfinder2gff.pl
find_ltr
batch_findltr.pl
cnv_findltr2gff.pl
ltr_seq
batch_ltrseq.pl
cnv_ltrseq2gff.pl
RepSeek
cnv_repseek2gff.pl
FINDMITE
batch_findmite.pl
cnv_findmite2gff.pl
Tandem Repeats Finder
batch_trf.pl
RepeatMasker
batch_mask.pl
batch_hardmask.pl
cnv_repmask2gff.pl
NCBI-BLAST
batch_blast.pl
batch_cnv_blast2gff.pl
cnv_blast2gff.pl
TE Nest
batch_tenest.pl
fetch_tenest.pl
cnv_tenest2gff.pl
HMMER
batch_hmmer.pl
Mathematically Defined Repeats
Requires the vmatch program
seq_oligocount.pl

Author: James Estill
Last Updated: September 29, 2011

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