Display Settings:

Format

Send to:

Choose Destination
We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Nucleic Acids Res. 2008 Jan;36(Database issue):D31-7. Epub 2007 Oct 16.

GISSD: Group I Intron Sequence and Structure Database.

Author information

  • 1State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, People's Republic of China.

Abstract

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; approximately 95% of them belong to the IC3 subgroup and reside in the chloroplast tRNA(Leu) gene. The GISSD database can be accessed at http://www.rna.whu.edu.cn/gissd/

PMID:
17942415
[PubMed - indexed for MEDLINE]
PMCID:
PMC2238919
Free PMC Article

Images from this publication.See all images (3)Free text

Figure 1.
Figure 2.
Figure 3.
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Icon for HighWire Icon for PubMed Central
    Loading ...
    Write to the Help Desk