Hello Scott and GMOD helpdesk --<div><br></div><div>I wanted to see if there would be an interest in the GMOD community for adding the DAWGPAWS plant genome annotation pipeline as a component of GMOD. </div><div><br></div>
<div>DAWGPAWS is a perl based annotation pipeline that seeks to facilitate annotation of genes and transposable elements in plant genomes. It thus includes gene annotation programs that are not part of some of the animal centric annotation pipelines, and has a larger focus on transposable element annotation. We used DAWGPAWS to annotate transposable elements in the maize genome, the genes and TEs in the wheat genome, and I'm now using the pipeline for annotation of genes and transposable elements in the Amborella genome. DAWGPAWS has been used by other labs to annotate multiple grass genomes, as well as cotton, strawberry, banana, sunflower, and the cucumber genome. </div>
<div><br></div><div>The manuscript describing DAWGPAWS is at:</div><div><a href="http://www.plantmethods.com/content/5/1/8">http://www.plantmethods.com/content/5/1/8</a></div><div>I am also writing a book chapter for annotation of retrotransposons in plants that will rely heavily on the use of DAWGPAWS tools.</div>
<div><br></div><div>Primary features of DAWGPAWS:</div><div> * facilitates splitting contigs for batch based annotation in a queue based cluster computing environment (ie. Platform LSF )</div><div> * incorporates ab initio and similarity search programs for gene annotation </div>
<div> * incorporates ab initio and similarity search programs for transposable element annotation as well as support for mathematically defined repeats</div><div> * provides tools for conversion of output from various programs into GFF2/GFF3 format output</div>
<div> - these generally all accept input from STDIN and write to STDOUT to facilitate use in other pipelines outside of DAWGPAWS</div><div> * provides tools for running annotation for sets of contigs in batch mode and converting output to GFF2/GFF3 format</div>
<div><br></div><div>The project page is at:</div><div><a href="http://dawgpaws.sourceforge.net/">http://dawgpaws.sourceforge.net/</a></div><div><br></div><div>The repository is at:</div><div><a href="http://dawgpaws.svn.sourceforge.net/viewvc/dawgpaws/">http://dawgpaws.svn.sourceforge.net/viewvc/dawgpaws/</a></div>
<div><br></div><div>A basic manual is at:</div><div><a href="http://dawgpaws.sourceforge.net/man.html">http://dawgpaws.sourceforge.net/man.html</a></div><div><br></div><div>I could write up a larger overview if you are interested, but thought I would first send a short email to see if there was any general interest in contributing DAWGPAWS into GMOD. DAWGPAWS is still in active development as part of my funded research related to annotation of the Amborella genome. I am currently adding code for gene model combiners such as EVM and developing a similar combiner for retrotransposons. </div>
<div><br></div><div>I am also generally interested in contributing additional support for transposable element annotation to the GMOD toolbox. I've developed some GBROWSE glyphs that I personally find helpful for display of transposable elements, and I would liked to see the future development of WebApollo incorporate visualization and annotation curation tools for transposable element annotation. </div>
<div><br></div><div>-- Jamie<br>-----------------------------------------<br>James C. Estill<br><a href="mailto:JamesEstill@gmail.com">JamesEstill@gmail.com</a><br><a href="http://jestill.myweb.uga.edu">http://jestill.myweb.uga.edu</a><br>
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