GISSD: Group I Intron Sequence and Structure Database. Export

@article{zhou08, 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/}, address = {State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, People's Republic of China.}, author = {Zhou, Y. and Lu, C. and Wu, Q. J. and Wang, Y. and Sun, Z. T. and Deng, J. C. and Zhang, Y.}, citeulike-article-id = {2719462}, citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/17942415}, citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=17942415}, issn = {1362-4962}, journal = {Nucleic acids research}, keywords = {database, groupi, ribozyme}, month = {January}, number = {Database issue}, posted-at = {2008-04-25 21:56:29}, priority = {0}, title = {GISSD: Group I Intron Sequence and Structure Database.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/17942415}, volume = {36}, year = {2008} }

TY - JOUR ID - zhou08 L3 - citeulike-article-id:2719462 N2 - 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/ IS - Database issue JF - Nucleic acids research SN - 1362-4962 AD - State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, People's Republic of China. TI - GISSD: Group I Intron Sequence and Structure Database. VL - 36 KW - database KW - groupi KW - ribozyme AU - Zhou, Y AU - Lu, C AU - Wu, QJ AU - Wang, Y AU - Sun, ZT AU - Deng, JC AU - Zhang, Y PY - 2008/01// UR - http://view.ncbi.nlm.nih.gov/pubmed/17942415 ER -