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Table 2 DAWGPAWS scripts for conversion of annotation results from native program output to GFF.

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

Annotation Program

Result Type

DAWGPAWS Script

FGENESH [50, 51]

Gene ab initio

cnv_fgenesh2gff.pl

GeneMark.hmm [43]

Gene ab initio

cnv_genemark2gff.pl

Find_LTR [45]

TE ab initio

cnv_findltr2gff.pl

LTR_FINDER [21]

TE ab initio

cnv_ltrfinder2gff.pl

LTR_seq [46]

TE ab initio

cnv_ltrseq2gff.pl

LTR_STRUC [20]

TE ab initio

cnv_ltrstruc2gff.pl

RepSeek [52]

TE ab initio

cnv_repseek2gff.pl

NCBI-BLAST [49]

TE and gene homology

cnv_blast2gff.pl

RepeatMasker [22]

TE homology

cnv_repmask2gff.pl

TEnest [24]

TE homology

cnv_tenest2gff.pl