KISS: the kinetoplastid RNA editing sequence search tool.

Kinetoplastid mitochondrial mRNA editing is a post-transcriptional process of uridine insertion and deletion. Editing is mediated by small RNA molecules termed guide RNAs (gRNAs). Most gRNAs are encoded by numerous small circular DNA minicircles, while the protein coding mitochondrial genes are encoded on a separate, larger genome called the maxicircle. In order to provide a workbench for the analysis of RNA editing in kinetoplastids and a well-annotated set of guide RNAs for Trypanosoma brucei, we generated the kinetoplastid RNA editing sequence search tool (KISS) (http://gmod.mbl.edu/kiss/). KISS is a pipeline and database that uses BLAST comparisons and minicircle sequence motifs to annotate potential gRNAs and cognate mRNA editing sequence. KISS 1.0 contains all previously known minicircle and maxicircle data from Trypanosoma brucei plus >400 new minicircle sequences. Using an online format, KISS 1.0 allows the mapping and visualization of all known T. brucei gRNAs to minicircle genes and to potential mRNA substrates for RNA editing.

[1]  S. Hajduk,et al.  Organization of minicircle genes for guide RNAs in trypanosoma brucei , 1990, Cell.

[2]  L. Simpson,et al.  Guide RNAs in kinetoplastid mitochondria have a nonencoded 3′ oligo(U) tail involved in recognition of the preedited region , 1990, Cell.

[3]  B. Sollner-Webb,et al.  RNA editing involves indiscriminate U changes throughout precisely defined editing domains , 1990, Cell.

[4]  K. Stuart,et al.  In vitro guide RNA/mRNA chimaera formation in Trypanosoma bruceiRNA editing , 1992, Nature.

[5]  P. Myler,et al.  Trypanosoma brucei minicircles encode multiple guide RNAs which can direct editing of extensively overlapping sequences. , 1993, Nucleic acids research.

[6]  K. Stuart,et al.  Multiple guide RNAs for identical editing of Trypanosoma brucei apocytochrome b mRNA have an unusual minicircle location and are developmentally regulated. , 1994, The Journal of biological chemistry.

[7]  Thomas Hermann,et al.  The guide RNA database , 1997, Nucleic Acids Res..

[8]  L. Simpson,et al.  The genomic organization of guide RNA genes in kinetoplastid protozoa: several conundrums and their solutions. , 1997, Molecular and biochemical parasitology.

[9]  Larry Simpson,et al.  U-insertion/deletion Edited Sequence Database , 1998, Nucleic Acids Res..

[10]  I. Longden,et al.  EMBOSS: the European Molecular Biology Open Software Suite. , 2000, Trends in genetics : TIG.

[11]  S. Lewis,et al.  The generic genome browser: a building block for a model organism system database. , 2002, Genome research.

[12]  Rodrigo Lopez,et al.  WU-Blast2 server at the European Bioinformatics Institute , 2003, Nucleic Acids Res..

[13]  L. Simpson,et al.  Genomic organization of Trypanosoma brucei kinetoplast DNA minicircles. , 2003, Protist.

[14]  Achim Schnaufer,et al.  Complex management: RNA editing in trypanosomes. , 2005, Trends in biochemical sciences.