DAWGPAWS Assists a Distributed Annotation Working Group (DAWG) in the sequence annotation of BAC sized contigs
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sequence annotate gene gene annotation annotate genes sequence annotation

DAWGPAWS Description

Assists a Distributed Annotation Working Group (DAWG) in the sequence annotation of BAC sized contigs DAWGPAWS is a suite of command line programs written in Perl that accelerates annotation of genes and transposable elements in plant genomes by automating the process of running annotation programs and facilitating combined evidence annotation curation.Since this suite of software was initially written to annotate randomly sampled wheat BACs, it is refered to as a Pipeline to Annoate Wheat Sequnces (PAWS). Although these programs have been initially designed for wheat, the scripts can also be easily applied to nearly any eukaryotic sequence annoation pipeline.The scripts in this suite are designed to facilitate high throughput generation of computational results for both gene annotation and transposable element annotation using a number of existing sequence anotation programs. These results are converted from the native output of the individual annotation programs to the standard GFF file format. Since a GFF file is a simple tab delmited text file, multiple computational results for a single sequence can easily be concatenated together using standard text maninpulation tools such as cat; proof that cats and dawgs can play well together. DAWGPAWS provides additional tools to facilitate using the Apollo Genome Annotation Curation Tool for visualization and curation of the computational results. Here are some key features of "DAWGPAWS": · FASTA file manipulation to prepare sequences for the annotation pipeline · Annotation of gaps in the sequence assemblies · Executing ab initio gene anotation and transposable element annotation programs in a high throughput pipeline · BLAST pipeline suitable for use in a cluster computing framework · Conversion of output from annotation software to the common GFF file format · Conversion of gff files to the game.xml format · Help is available in all command line programs using command line flags. Help info and full manual files are still under development for some programs · Manual pages for the individual programs are available on the DAWGPAWS web site and are including in the Release-1.0 download of the DAWGPAWS suite.

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