DAWGPAWS

1.0 GPL (GNU General Public License)    
  UNRATED

  473 downloads

A suite of command line programs written in Perl that accelerates annotation of genes and transposable elements in plant genomes

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The scripts in the DAWGPAWS suite are designed to facilitate high throughput generation of computational results for both geneDAWGPAWS is a suite of scripts written in Perl that are desinged to assist a Distributed Annotation Working Group (DAWG) in the sequence annotation of BAC sized contigs. 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 were initially designed for wheat, the scripts can be applied to nearly any eukaryotic sequence annoation pipeline.

The scripts in the DAWGPAWS 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.

Usage of DAWGPAWS is through a series of command line programs. A command line interface was chosen since these programs will usually be run remotely on high preformance machines running some version of the Unix/Linux operating system. Since a command line inteface has been written for all programs, no special knowledge of Perl is required to use this suite. However, since some the Perl scripts rely on external Perl modules, a working knowledge of Perl will be helpful when installing DAWGPAWS.

How to Cite DAWGPAWS

A manuscript has been submitted describing the DAWGPAWS program. Until this manuscript is published, please refer to the DAWGPAWS SourceForge website when describing your use of this program.

JC Estill and JL Bennetzen. 2009. The DAWGPAWS Pipeline for the Annotation of Genes and Transposable Elements in Plant Genomes. http://dawgpaws.sourceforge.net/

Supported Annotation Programs

DAWGPAWS includes scripts to work with computational evidences from the following standalone programs and web sites. You can get information for the following programs by clicking on the annotation program name, and you can get the documentation for the DAWGPAWS script by clicking on the script name. For full information on installing and using these programs, see the DAWGPAWS manual.

These annotation programs are not included in the DAWGPAWS program and must be installed separately.
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Last updated on May 13th, 2009

#gene annotation #transposable elements #plant plant #gene #annotation #transposable #elements

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