BioBloom Tools (BBT) provides the means to create filters for a given reference and then to categorizes sequences. This methodology is faster than alignment but does not provide mapping locations. BBT was initially intended to be used for pre-processing and QC applications like contamination detection, but is flexible to accommodate other purposes.
SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatranscriptomic data produced by next-generation sequencers. It is capable of handling large RNA databases and sorting out all fragments matching to the database with high accuracy and specificity.
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.
The AgilentFilter program is a tool for filtering and reformatting the raw data .txt files from the Agilent microarray platform. Have you ever wanted to remove the positive and negative control spots from a data set, or extract just the gene annotations and pertinent data columns from a set of Agilent array files, or filter out any weak or low quality spots from an Agilent data set?