RNAsifter

Current Version: 1.0

RNAsifter is a non-rigorous filter for the rfam database, that is based on the abstract shape approach. It exploits the familily specific secondary structure, i.e. it computes shapes for the query-sequence and compares them to a precalculated shape-index. The exact matches deliver - hopefully only few - candiate families in which the query-sequence might fold. Membership for the candidate families is checked with the program cmsearch, afterwards.

Note: Due to the extremly high runtime of the underlying cmsearch, submission is restricted to a maximal sequencelength of 500 bases and maximal 50 sequences in a multiple fasta file.

RNAsifter is also available as Perl source code. Requirements for local usage are:

• RNAshapes
• cmsearch from the infernal package
• and the model-files with the thresholdfile Rfam.thr from rfam.