Skip Navigation



Bioinformatics Advance Access published online on December 10, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti207
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
21/8/1393    most recent
bti207v1
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 Wahl, M. B.
Right arrow Articles by Imai, K.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Wahl, M. B.
Right arrow Articles by Imai, K.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics © Oxford University Press 2004; all rights reserved.
Received September 4, 2004
Revised November 23, 2004
Accepted December 2, 2004

Article

LongSAGE analysis significantly improves genome annotation: identifications of novel genes and alternative transcripts in the mouse

Matthias B. Wahl 1, Ulrich Heinzmann 2, and Kenji Imai 1*

1 Institute of Developmental Genetics, GSF-National Research Center for Environment and Health, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
2 Institute of Pathology, GSF-National Research Center for Environment and Health, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany

* To whom correspondence should be addressed.
Kenji Imai, E-mail: imai{at}gsf.de


  Abstract

Motivation: Because of its increased tag length, LongSAGE tags are expected to be more reliable in direct assignment to genome sequences. Therefore, we evaluated the use of LongSAGE data in genome annotation by using our LongSAGE dataset of 202,015 tags (consisting of 41,718 unique tags), experimentally generated from mouse embryonic tail libraries.

Results: A fraction of LongSAGE tags could not be unambiguously assigned to its gene, due to the presence of widely conserved sequences downstream of particular CATG anchor sites. The presence of alternative forms of transcripts was confirmed in 45% of all detected genes. Surprisingly, a large fraction of LongSAGE tags with hits to the genome (66%) could not be assigned to any gene annotated in EnsEMBL. Among such cases, 2,098 LongSAGE tag fell into a region containing a putative gene predicted by GenScan, providing experimental evidence for the presence of real genes, while 9,112 genes were found out to be left out or wrongly annotated by the EnsEMBL pipeline.

Conclusions: LongSAGE transcriptome data can significantly improve the genome annotation by identifying novel genes and alternative transcripts, even in the case of thus far best-characterized organisms like the mouse.


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
 IOVSHome page
C. Bowes Rickman, J. N. Ebright, Z. J. Zavodni, L. Yu, T. Wang, S. P. Daiger, G. Wistow, K. Boon, and M. A. Hauser
Defining the Human Macula Transcriptome and Candidate Retinal Disease Genes Using EyeSAGE
Invest. Ophthalmol. Vis. Sci., June 1, 2006; 47(6): 2305 - 2316.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
M. B. Wahl, U. Heinzmann, and K. Imai
LongSAGE analysis revealed the presence of a large number of novel antisense genes in the mouse genome
Bioinformatics, April 15, 2005; 21(8): 1389 - 1392.
[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.