title: KISS: the kinetoplastid RNA editing sequence search tool.
abstract: 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.
authors.affiliation: Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA.
authors.forename: Torsten
authors.initials: T
authors.lastname: Ochsenreiter
authors.forename: Michael
authors.initials: M
authors.lastname: Cipriano
authors.forename: Stephen L
authors.initials: SL
authors.lastname: Hajduk
mesh_terms: D000818:Animals; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D030561:Databases, Nucleic Acid; D020407:Internet; D016830:Kinetoplastida / Q000235:genetics / Q000378:metabolism; D017393:RNA Editing; D017394:RNA, Guide, Kinetoplastida / Q000737:chemistry* / Q000235:genetics; D016053:RNA, Protozoan / Q000737:chemistry* / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*; D014346:Trypanosoma brucei brucei / Q000235:genetics* / Q000378:metabolism
chemical_list: D016053:RNA, Protozoan; D017394:RNA, Guide, Kinetoplastida