Nucleic Acids Research Advance Access originally published online on October 16, 2007
Nucleic Acids Research 2008 36(Database issue):D31-D37; doi:10.1093/nar/gkm766
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2008, Vol. 36, Database issue D31-D37
© 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.
Articles |
GISSD: Group I Intron Sequence and Structure Database
1State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, People's Republic of China and 2LRI, UMR CNRS 8623, Université Paris-Sud 11 F91405 Orsay Cedex, France
* To whom correspondence should be addressed. Tel: +86 27 68756207; Fax: +86 27 68754945; Email: yizhang{at}whu.edu.cn The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors.
Received August 15, 2007. Revised September 7, 2007. Accepted September 11, 2007.
Group I Intron Sequence and Structure Database (GISSD) is a specialized and comprehensive database for group I introns, focusing on the integration of useful group I intron information from available databases and providing de novo data that is essential for understanding these introns at a systematic level. This database presents 1789 complete intron records, including the nucleotide sequence of each annotated intron plus 15 nt of the upstream and downstream exons, and the pseudoknots-containing secondary structures predicted by integrating comparative sequence analyses and minimal free energy algorithms. These introns represent all 14 subgroups, with their structure-based alignments being separately provided. Both structure predictions and alignments were done manually and iteratively adjusted, which yielded a reliable consensus structure for each subgroup. These consensus structures allowed us to judge the confidence of 20 085 group I introns previously found by the INFERNAL program and to classify them into subgroups automatically. The database provides intron-associated taxonomy information from GenBank, allowing one to view the detailed distribution of all group I introns. CDSs residing in introns and 3D structure information are also integrated if available. About 17 000 group I introns have been validated in this database; 
95% of them belong to the IC3 subgroup and reside in the chloroplast tRNALeu gene. The GISSD database can be accessed at http://www.rna.whu.edu.cn/gissd/
The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors.