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DAWGPAWS specifications

Information


Unique identifier OMICS_09443
Name DAWGPAWS
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.1
Stability Beta
Requirements
BioPerl
Maintained Yes

Versioning


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Documentation


Maintainer


  • person_outline James C. Estill <>

Publication for DAWGPAWS

DAWGPAWS in publications

 (4)
PMCID: 3219971
PMID: 21619600
DOI: 10.1186/gb-2011-12-5-r48

[…] to 8 × coverage on an abi 3730xl sequencer. gaps were closed for each scaffold, and contiguous 487,318 and 629,678 bp phase ii sequences were assembled for contigs 431 and 1003, respectively., the dawgpaws suite of scripts was used to organize ab initio gene predictions, blast results and the output of repeat identification tools [,]. ab initio gene predictions were generated using fgenesh [], […]

PMCID: 3163431
PMID: 21470968
DOI: 10.1093/molbev/msr080

[…] supplementary table s2, supplementary material online)., gaps between scaffolds were closed by adding 50 ns to generate a contiguous sequence for each bac. the bac sequences were run through the dawgpaws pipeline, which does ab initio as well as homology-based identification of genes and tes (). the dawgpaws output file was visualized in apollo (), and gene models were annotated manually. […]

PMCID: 3095328
PMID: 21073723
DOI: 10.1186/1471-2229-10-246

[…] 16 bp (tetranucleotides), 20 bp (pentanucleotides) and 24 bp (hexanucleotides)., transposons were annotated using ab initio and sequence similarity searches integrated in a pipeline based on dawgpaws []. the programs used for de novo prediction of ltr retrotransposons included ltr_struc [], ltr_finder [] and ltr_seq [], and vary in the type of structures they look for, their stringency […]

PMCID: 2774510
PMID: 19936065
DOI: 10.1371/journal.pgen.1000732

[…] in the maize agp were downloaded from genbank. full-length ltr retrotransposons were identified by ltr_struc and mapped onto these bacs through the use of batch annotation scripts available in the dawgpaws annotation package . this process resulted in a database of 35,229 full-length ltr retrotransposons., the 5′ ltr sequences of this dataset of full-length ltr retrotransposons were used […]


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DAWGPAWS institution(s)
Department of Plant Biology, The University of Georgia, Athens, GA, USA; Department of Genetics, The University of Georgia, Athens, GA, USA

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