The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes

Table 1 DAWGPAWS annotation scripts for generating computational annotation results in batch mode.

Annotation Program	Result Type	DAWGPAWS Script
EuGène [9]	Gene ab initio and automated combined evidence	batch_eugene.pl
GeneID [42]	Gene ab initio	batch_geneid.pl
GeneMark.hmm [43]	Gene ab initio	batch_genemark.pl
Genscan [44]	Gene ab initio	batch_genescan.pl
Find_LTR [45]	TE ab initio	batch_findltr.pl*
LTR_STRUC [20]	TE ab initio	batch_ltrstruc.vbs
LTR_FINDER [21]	TE ab initio	batch_ltrfinder.pl*
LTR_seq [46]	TE ab initio	batch_ltrseq.pl*
FINDMITE [19]	TE ab initio	batch_findmite.pl*
Tandem Repeats Finder [47]	Repeat ab initio	batch_trf.pl
HMMER [48]	TE homology	batch_hmmer.pl*
NCBI-BLAST [49]	TE and gene homology	batch_blast.pl*
RepeatMasker [22]	TE homology	batch_repmask.pl*
TEnest [24]	TE homology	batch_tenest.pl

These scripts operate on a directory of FASTA files, and generate the native results of the annotation program as well as the GFF file format. The exception is the batch_ltrstruc.vbs visual basic script that must be used in conjunction with cnv_ltrstruc2gff.pl to generate results in GFF.
* Indicates programs that make use of a configuration file. The nature and format of the configuration file for these programs is described in the individual help file for those programs.

ISSN: 1746-4811