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

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

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
  1. 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.
  2. * 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.