DAWGPAWS / News: Recent posts

The project webpage has been updated at http://http://dawgpaws.sourceforge.net/. Additional information will be added for gene and TE annotation in the coming weeks.

I released a beta version of DAWGPAWS-1.1. This includes the ability to convert output to GFF3 format with the gff-ver option. The documentation for most programs will need to be updated, and many of the test files will need to be updated. However, much of the core functionality of the programs should work in the beta version.

The modified find_ltr.pl program for interfacing with DAWGPAWS is now available at
http://darwin.informatics.indiana.edu/cgi-bin/evolution/MGEScan_LTR.pl

It looks like NCBI just implemented a major change in command line BLAST. These changes are not supported by the current version of DAWGPAWS. Please download the legacy version of command line blast at ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.17/ for use with the DAWGPAWS program.

DAWGPAWS has now been published in the journal Plant Methods.

The article is at http://www.plantmethods.com/content/5/1/8

The PubMed link is http://www.ncbi.nlm.nih.gov/pubmed/19545381

DAWGPAWS has now been published in the journal Plant Methods.

The article is at http://www.plantmethods.com/content/5/1/8

The PubMed link is http://www.ncbi.nlm.nih.gov/pubmed/19545381

The program tsd_check.pl was added to subversion code base. This program will check an annotated file of transposable elements for Target Site Duplications.

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.

I have just uploaded Release 1.0 of this package.

I recently replaced the cnv_fgenesh2gff program with a new version that makes use of the bioperl module for converting fgenesh output. This new version uses the standard dawgpaws command line options, and will attempt to strip HTML tags when present. This should therefore be able to use results saved in html from the softberry web site.

Added batch_trf.pl script to run the Tandem Repeats Finder program in batch mode. This currently uses a hard coded variable set, and only allows for one set of parameters.

I have added the batch_eugene.pl program to run the EuGene program in batch mode. This currently only generates the gene model predictions and does not use additional modules to expand these models. These results will currently be different the the TriAnnot results due to differences in the parameters files.

Added the script batch_geneid.pl to run the geneid program in batch mode on your local machine. This also translates the gff2 format from geneid to a gff format that Apollo can use. This script still needs POD documentation.

Added batch_tenest.pl to run the TENest program in batch mode following the general DAWG-PAWS paradigm.

Made update to batch_oligocount.pl to use a config file in batch mode on a directory of fasta format sequences. The config file allows for control of: (1) the word length
(2) Name of the database to use
(3) Path to the mkvtree index file to use.

The output now includes:
(1) The native vmatch output,
(2) a gff format file of the counts for each oligo of size k,
(3) a fasta like count file similar to PHRED *.qual files.... read more

The batch_ltrfinder.pl program now extracts the sequences of the features identified by LTR Finder and places them in the ltr_finder directory. This code needs to be cleaned up and should be converted to an Object Oriented Perl approach but the current version does work.

Adding tests to the SVN for DAWG-PAWS.

These will be in the directory
/trunk/t
and will make use of data in
/trunk/t/data

I am currently in the process of adding and updating POD documentation to the DAWG-PAWS scripts. These docs will be converted to html and made available on the project web page.

The DAWG-PAWS website has been added to Sourcefoge.

http://dawgpaws.sourceforge.net/

The SVN repository has been successfully migrated from the old google web site to the subversion repository hosted by SourceForge.