Genome Research cityscape

Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
QUICK SEARCH:   [advanced]


     

This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
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 Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Jareborg, N.
Right arrow Articles by Durbin, R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Jareborg, N.
Right arrow Articles by Durbin, R.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us   Add to Digg   Add to Reddit   Add to Technorati  
What's this?

Vol. 10, Issue 8, 1148-1157, August 2000

LETTER
Alfresco---A Workbench for Comparative Genomic Sequence Analysis

Niclas Jareborg,1,2,3 and Richard Durbin1

1 The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom; 2 Center for Genomics Research, Karolinska Institutet, S-171 77 Stockholm, Sweden

Comparative analysis of genomic sequences provides a powerful tool for identifying regions of potential biologic function; by comparing corresponding regions of genomes from suitable species, protein coding or regulatory regions can be identified by their homology. This requires the use of several specific types of computational analysis tools. Many programs exist for these types of analysis; not many exist for overall view/control of the results, which is necessary for large-scale genomic sequence analysis. Using Java, we have developed a new visualization tool that allows effective comparative genome sequence analysis. The program handles a pair of sequences from putatively homologous regions in different species. Results from various different existing external analysis programs, such as database searching, gene prediction, repeat masking, and alignment programs, are visualized and used to find corresponding functional sequence domains in the two sequences. The user interacts with the program through a graphic display of the genome regions, in which an independently scrollable and zoomable symbolic representation of the sequences is shown. As an example, the analysis of two unannotated orthologous genomic sequences from human and mouse containing parts of the UTY locus is presented.

3 Corresponding author.

10:1148-1157 ©2000 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/00 $5.00
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg   Add to Reddit Reddit   Add to Technorati Technorati    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
Y. J. K. Edwards, T. J. Carver, T. Vavouri, M. Frith, M. J. Bishop, and G. Elgar
Theatre: a software tool for detailed comparative analysis and visualization of genomic sequence
Nucleic Acids Res., July 1, 2003; 31(13): 3510 - 3517.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
C. Liu, T. I. Bonner, T. Nguyen, J. L. Lyons, S. L. Christian, and E. S. Gershon
DNannotator: annotation software tool kit for regional genomic sequences
Nucleic Acids Res., July 1, 2003; 31(13): 3729 - 3735.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Aerts, G. Thijs, B. Coessens, M. Staes, Y. Moreau, and B. D. Moor
Toucan: deciphering the cis-regulatory logic of coregulated genes
Nucleic Acids Res., March 15, 2003; 31(6): 1753 - 1764.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
U. DeSilva, L. Elnitski, J. R. Idol, J. L. Doyle, W. Gan, J. W. Thomas, S. Schwartz, N. L. Dietrich, S. M. Beckstrom-Sternberg, J. C. McDowell, et al.
Generation and Comparative Analysis of ~3.3 Mb of Mouse Genomic Sequence Orthologous to the Region of Human Chromosome 7q11.23 Implicated in Williams Syndrome
Genome Res., January 1, 2002; 12(1): 3 - 15.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. D. Wilson, C. Riemer, D. W. Martindale, P. Schnupf, A. P. Boright, T. L. Cheung, D. M. Hardy, S. Schwartz, S. W. Scherer, L.-C. Tsui, et al.
Comparative analysis of the gene-dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5
Nucleic Acids Res., March 15, 2001; 29(6): 1352 - 1365.
[Abstract] [Full Text] [PDF]


Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
Genes Dev. Learn. Mem.
Protein Science RNA Genome Res.