Skip Navigation



Bioinformatics Advance Access published online on October 6, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti705
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
21/23/4302    most recent
bti705v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Dávila, A. M. R.
Right arrow Articles by Campos, M. L. M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Dávila, A. M. R.
Right arrow Articles by Campos, M. L. M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received July 10, 2005
Revised September 7, 2005
Accepted October 5, 2005

Applications note

GARSA: Genomic Analysis Resources for Sequence Annotation

Alberto M. R. Dávila 1*, Daniel M. Lorenzini 2, Pablo N. Mendes 3, Thiago S. Satake 4, Gabriel R. Sousa 1, Linair M. Campos 3, Camila J. Mazzoni 1, Glauber Wagner 1, Paulo F. Pires 3, Edmundo C. Grisard 2, Maria C. R. Cavalcanti 5, and Maria Luiza M. Campos 3

1 DBBM, Instituto Oswaldo Cruz, Fiocruz, Brazil
2 Lab. de Bioinformática & Lab. de Protozoologia - MIP/CCB, Universidade Federal de Santa Catarina, Brazil
3 Departamento de Ciência da Computação/Núcleo de Computação Eletrônica - UFRJ, Brazil
4 Engenharia de Bioprocessos e Biotecnologia, Universidade Federal do Paraná, Brazil
5 Instituto Militar de Engenharia, Brazil

* To whom correspondence should be addressed.
Alberto M. R. Dávila, E-mail: davila{at}fiocruz.br


  Abstract

Summary: The growth of genome data and analysis possibilities have brought new levels of difficulty for scientists to understand, integrate and deal with all this ever-increasing information. In this scenario, GARSA has been conceived aiming to facilitate the tasks of integrating, analyzing and presenting genomic information from several Bioinformatics tools and Genomic databases, in a flexible way. GARSA is a user-friendly web-based system designed to analyze genomic data in the context of a pipeline. EST and GGS data can be analysed using the system since it accepts: a) chromatograms, b) download of sequences from GenBank, c) Fasta files stored locally or d) a combination of all 3. Quality evaluation of chromatograms, vector removing and clusterization are easily performed as part of the pipeline. A number of local and customizable Blast and CDD analyses can be performed as well as Interpro, complemented with phylogeny analyses. GARSA is being used for the analyses of Trypanosoma vivax (GSS and EST), T. rangeli (GSS, EST and ORESTES), Bothrops jararaca (EST), Piaractus mesopotamicus (EST) and Lutzomyia longipalpis (EST).

Availability: The GARSA system is freely available under GPL license1. For download requests visit http://www.biowebdb.org/garsa/ or contact Dr. Alberto Dávila.

1 http://www.biowebdb.org/garsa/
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
A. C. Stewart, B. Osborne, and T. D. Read
DIYA: a bacterial annotation pipeline for any genomics lab
Bioinformatics, April 1, 2009; 25(7): 962 - 963.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.