GISSD: Group I Intron Sequence and Structure Database.
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/
Zhou
Yu
Y
State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, People's Republic of China.
Lu
Chen
C
Wu
Qi-Jia
QJ
Wang
Yu
Y
Sun
Zhi-Tao
ZT
Deng
Jia-Cong
JC
Zhang
Yi
Y
D030561:Databases, Nucleic Acid; D020407:Internet; D007438:Introns; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D022661:RNA, Untranslated / Q000145:classification; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D014584:User-Computer Interface
D022661:RNA, Untranslated