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Table 3 Additional helper scripts included in the DAWGPAWS package.

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

DAWGPAWS Script Purpose Converts GFF files to the game.xml format. Converts game.xml files to the GFF3 format. Given a directory of lowercase masked sequence files, this will replace lowercase residues with an N or X to indicate masking. Given annotation results scattered across multiple directories, this program can merge the results into subdirectories in a single parent directory. Given GFF annotation results from multiple methods, this program generates a Euler Diagram of these features using the VennMaster program [55] This program will annotate gaps in the query sequences in the input directory. This program writes shell scripts to run DAWGPAWS in a cluster environment running the Platform LSF queuing system. Given a FASTA file with multiple sequence files, this program generates a separate FASTA file for each sequence record. The sequence files produced are named using the sequence ID in the FASTA header in the input file. This program merges all FASTA files in a directory into a single FASTA file. This program shortens the FASTA header by limiting the header length, or splitting the header by a delimiting character. Some annotation programs are limited by the length of the FASTA header that is accepted, and this programs allows input files to meet this limitation. Fetches multiple results from the Plant GDB TEnest server and converts the results to GFF. Given a GFF file that contains point or segment data, this will extract segments with score values that exceed a threshold value. Because the LTR_STRUC program only runs under the windows environment, this program converts FASTA sequences in UNIX to DOS line endings and generates the files name and flist file required for LTR_STRUC. This program allows for the generation of a GFF file that counts the number of times an oligomer in the genomic contig occurs in a reference shotgun sequence database.