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Description
DAWGPAWS is a tool for discovering the location of the genes
and transposable elements in eukaryotic genomic sequences. It
is distributed as a suite of command line programs that are
designed to assist a Distributed Annotation Working Group
(DAWG) in the annotation of genomic sequence contigs. These
programs generate the multiple tracks of annotation evidence
that can be computationally combined or manually curated to
generate gene models and richly annotated transposable element
predictions. The computation of the annotation evidence tracks
can be distributed across nodes in a high-performance
computing environment providing a scalability that makes this
a Pipeline to Annotate Whole-genome Sequences (PAWS). The
flexibility of evidences that can be generated by DAWGPAWS
allows it to be applied to any eukaryotic genome annotation
effort.
Features
DAWGPAWS uses a command line interface for all programs. The command line interface was chosen since computational annotation processes will usually be performed remotely on high-performance computing clusters. Since a standardized command line interface has been written for all programs, no prior knowledge of Perl is required to use this suite.
The current features of DAWGPAWS include:
- FASTA file manipulation to prepare sequences for the
annotation pipeline
- Annotation of gaps in the sequence assemblies
- Executing ab initio gene annotation 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 GFF file format
- GFF2 and GFF3 are both supported output formats
- 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. To access help where
prognameis the name of the individual program:
progname --usage
generate a basic usage message with info on the required arguments
progname --help
generate a more extensive help message that includes required arguments and all options
progname --man
view the full manual for the program- 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.
User Manual and Software Documentation
A comprehensive user manual describing the use of DAWGPAWS
for genome annotation is available from the DAWGPAWS
web site on SourceForge. This manual is also included in
the release 1.0 version of the DAWGPAWS program.
How to Cite DAWGPAWS
If you use DAWGPAWS in your annotation efforts, you should
cite the DAWGPAWS manuscript published in Plant Methods:
JC Estill and JL Bennetzen. 2009. "The DAWGPAWS pipeline for
the annotation of genes and transposable elements in plant
genomes." Plant
Methods. 5:8.
| Author: James
Estill Last Updated: September 28, 2011 |
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