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Project Scripts

The following is the previous documentation on this site.

Introduction

This is the code repository for DAWG-PAWS A Distributed Annotation Working Group Pipeline to Annotate Wheat Sequences. DAWG-PAWS is a set of command line programs written in Perl and is released under version 3 of the GNU General Public License. Scripts in development are available for individual download at the project's subversion repository. These scripts are not all stable and are subject to change without notice. Information for downloading the entire set of scripts is available in the project's Source section.

The DAWG-PAWS program assumes that you are annotating BAC sized contigs of a plant genome. The process treats each contig as a separate unit of analysis.

A number of programs that may be useful a la carte include:

• cnv_tenest2gff.pl - Convert TE Nest output to gff format.
• batch_findmite.pl - Run the findmite program in batch mode.
• batch_mask.pl - Run the RepeatMasker program in batch mode.

General Annotation Software

• Apollo - Apollo is a genome annotation curation tool. The Apollo program is the main workbench for visualizing all gff output from the DAWG-PAWS scripts.

TE Annotation Software

• FIND_LTR
• ltr_finder.pl
• FINDMITE