CIWOG: Common Introns Within Orthologous Genes
Software and Databases



Description

The residence of spliceosomal introns within protein-coding genes can fluctuate over time, with genes gaining, losing, or conserving introns in a complex process that is not entirely understood. One approach for studying intron evolution is to compare introns with respect to position and type within closely related genes. CIWOG (Common Introns Within Orthologous Genes) is software that detects common introns in protein-coding genes based on position and sequence conservation in the corresponding protein alignments. CIWOG provides dynamic web displays that facilitate detailed intron studies within orthologous genes. User-supplied options control how introns are clustered into sets of common introns. CIWOG also identifies special classes of introns, in particular those with GC- or U12-type donor sites, which enables analyses of these introns in relation to their counterparts in the other genes in orthologous groups.

Several pre-computed CIWOG databases are available below. Click on a database to enter the web displays.

CIWOG Databases

Title Date Description Associated Publication(s)
CIWOG_Plants_Version_2 6/15/2010 - In process
CIWOG_Plants_Version_1_loose 5/11/2009 29,967 orthologous gene clusters from eight plant species. Introns clustered within one alignment position and one gap. Wilkerson, M.D., Ru, Y., and Brendel, V.P. (2009)
Common introns within orthologous genes: software and application to plants
Briefings in Bioinformatics, 10(6), 631-644.
CIWOG_Plants_Version_1_strict 5/11/2009 29,967 orthologous gene clusters from eight plant species. Introns clustered at identical alignment positions. Wilkerson, M.D., Ru, Y., and Brendel, V.P. (2009)
Common introns within orthologous genes: software and application to plants
Briefings in Bioinformatics, 10(6), 631-644.

Software

Download CIWOG software for local installations or custom datasets.

Credits

If you use these software or databases, please cite Wilkerson, MD et al (2009) Common introns within orthologous genes: software and application to plants. Briefings in Bioinformatics, 10(6), 631-644.

Research was supported by : NSF DBI-0606909