GISSD -- Group I Intron Sequence and Structure Database

What you can do:
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.
Highlights:
  • Aims to provide a consensus structure for each subgroup of group I introns based on high quality alignments, to judge the confidence of the group I introns annotated by Rfam, to classify Rfam group I introns into subgroups based on the consensus structures, and to provide intron number-containing taxonomy tree based on the taxonomy information of the host organisms of all group I introns.
  • Currently, GISSD presents 1789 intron complete records, including the nucleotide sequence of each annotated intron plus 15 nt of the upstream and downstream exons, as well as the pseudoknots-containing secondary structure predicted by integrating comparative sequence analysis and minimal free energy algorithms.
  • These introns represent all 13 known minor subgroups and an undifferentiated major subgroup, with their structure-based alignments being separately provided.
  • Both structure predictions and alignments were done manually and iteratively adjusted, which yielded reliable consensus structure for each subgroup allowing us to judge the confidence of 20,085 group I introns previously predicted by INFERNAL program, and to classify these large amount of introns into subgroups automatically.
  • The database provides the intron-associated taxonomy information from GenBank, allowing one to detailedly view the distribution of all group I introns.
  • CDSs residing in introns and 3-D structure information are also integrated if available.
Keywords:
  • introns
  • INFERNAL
  • structure prediction
  • structure-based alignment
  • group I intron
Literature & Tutorials:
This record last updated: 02-18-2008

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