On the identification of group II introns in nucleotide sequence data

Journal of Molecular Biology
V KnoopA Brennicke

Abstract

Four different consensus sequences (GTI, group II identifiers) have been derived from domains V of known group II introns and are used as query input sequences for sensitive database screenings with the FASTA and LFASTA programs. The set of four GTI sequences can identify all domains V of the 96 known group II introns in the completely sequenced chloroplast genomes of Marchantia polymorpha, Epifagus virginiana, Oryza sativa, Nicotiana tabacum and the completely sequenced mitochondrial genomes of Saccharomyces cerevisiae, Podospora anserina, Schizosaccharomyces pombe and Marchantia polymorpha. Seven moderately high-scoring hits can easily be rejected as false-positives since they do not fulfil secondary structure requirements. Large FASTA outputs obtained after screening the entire nucleotide sequence database are evaluated in a second step by a program (D5SCAN) that allows the assignment of variable selection criteria for potential domain V secondary structures. Database searches with these routines yield evidence for several group II intron sequences previously unrecognized. These include novel intron structures in the cyanobacterium Synechocystis and in the mitochondrial genomes of Marchantia, soybean, pea, broad bean, sugar ...Continue Reading

Citations

Jan 1, 1995·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·M S Gelfand
Jan 15, 1997·Nucleic Acids Research·C Carrillo, L Bonen
Jan 24, 2008·PloS One·Yvonne VallèsJeffrey L Boore
Oct 25, 2003·Proceedings of the National Academy of Sciences of the United States of America·Jonathan GallantDale Lindsley
Jan 21, 1997·Proceedings of the National Academy of Sciences of the United States of America·O MalekV Knoop
Dec 28, 1999·Proceedings of the National Academy of Sciences of the United States of America·P Giegé, A Brennicke
Mar 24, 2005·Journal of Molecular Evolution·Teresa M R ReginaCarla Quagliariello
Dec 21, 2000·Molecular Microbiology·F Martínez-Abarca, N Toro
Apr 9, 2001·Comptes rendus de l'Académie des sciences. Série III, Sciences de la vie·P Giegé, A Brennicke

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