Package: wnpp
Severity: wishlist
* Package name : baitfisher
Version : 1.0
Upstream Author : Christoph Mayer
* License : GPL
Programming Lang: C++
Description : package for designing hybrid enrichment probes
The BaitFisher package consists of two programs: BaitFisher and
BaitFilter.
BaitFisher was been designed to construct hybrid enrichment baits from
multiple sequence alignments (MSAs) or annotated features in MSAs. The
main goal of BaitFisher is to avoid redundancy in the construction of
baits by designing fewer baits in conserved regions of the MSAs and
designing more baits in variable regions. This makes use of the fact
that hybrid enrichment baits can differ to some extends from the target
region, which they should capture in the enrichment procedure. By
specifying the allowed distance between baits and the sequences in the
MSAs the user can control the allowed bait-to-target distance and the
degree of reduction in the number of baits that are designed. See the
BaitFisher paper for details.
BaitFilter was designed (i) to determine whether baits bind
unspecifically to a reference genome, (ii) to filter baits that only
have partial length matches to a reference genome, (iii) to determine
the optimal bait region in a MSA and to convert baits to a format that
can be uploaded at a bait constructing company. The optimal bait region
can be the most conserved region in the MSA or the region with the
highest number of sequences without gaps or ambiguous nucleotides.