RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences.

ABSTRACT:

Background

Repeat-induced point mutation (RIP) is a fungal-specific genome defence mechanism that alters the sequences of repetitive DNA, thereby inactivating coding genes. Repeated DNA sequences align between mating and meiosis and both sequences undergo C:G to T:A transitions. In most fungi these transitions preferentially affect CpA di-nucleotides thus altering the frequency of certain di-nucleotides in the affected sequences. The majority of previously published in silico analyses were limited to the comparison of ratios of pre- and post-RIP di-nucleotides in putatively RIP-affected sequences - so-called RIP indices. The analysis of RIP is significantly more informative when comparing sequence alignments of repeated sequences. There is, however, a dearth of bioinformatics tools

SUBMITTER: Hane JK 

PROVIDER: S-EPMC2621366 | biostudies-literature | 2008 Nov

REPOSITORIES: biostudies-literature