Skip Navigation



Bioinformatics Advance Access published online on February 3, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm023
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrowOA All Versions of this Article:
23/7/903    most recent
btm023v1
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
Google Scholar
Right arrow Articles by Galante, P. A. F.
Right arrow Articles by Kuo, W. P.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Galante, P. A. F.
Right arrow Articles by Kuo, W. P.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Automatic Correspondence of Tags and Genes (ACTG): A Tool for the Analysis of SAGE, MPSS, and SBS Data

Pedro A. F. Galante a,b,*, Jeff Trimarchi c, Constance L. Cepko c,d, Sandro J. de Souza b, Lucila Ohno-Machado e,f and Winston P. Kuo e,g

a Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
b Laboratory of Computational Biology, Ludwig Institute for Cancer Research, São Paulo Branch
c Department of Genetics, Harvard Medical School
dHoward Hughes Medical Institute, Harvard Medical School
e Decision Systems Group, Brigham and Women’s Hospital
f Division of Health Sciences and Technology, Harvard Medical School and MIT
g Department of Organismic and Evolutionary Biology/FAS, Harvard University

*To whom correspondence should be addressed. Pedro Galante, E-mail: pgalante{at}ludwig.org.br


  Abstract

Summary: A critical step in any SAGE, MPSS, and SBS data analysis is tag-to-gene assignment. Current available tools are limited by a tag-by-tag annotation process and/or do not provide the dataset that is used to produce a complete tag-to-gene mapping. We developed ACTG, a web-based application that allows a large-scale tag-to-gene mapping using several reference data sets. ACTG can annotate SAGE (14 bps or 21 bps), MPSS (17 bps or 20 bps), and SBS (16 bp) data for both human and mouse genomesorganisms.

Availability: http://retina.med.harvard.edu/ACTG/

Associate Editor: John Quackenbush

Received on October 23, 2006; revised on December 22, 2006; accepted on January 19, 2007

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
 Hum Mol GenetHome page
S. Thomas, M. Thomas, P. Wincker, C. Babarit, P. Xu, M. C. Speer, A. Munnich, S. Lyonnet, M. Vekemans, and H. C. Etchevers
Human neural crest cells display molecular and phenotypic hallmarks of stem cells
Hum. Mol. Genet., November 1, 2008; 17(21): 3411 - 3425.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T. Norambuena, R. Malig, and F. Melo
SAGExplore: a web server for unambiguous tag mapping in serial analysis of gene expression oriented to gene discovery and annotation
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W163 - W168.
[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.