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Package: baitfisher (1.2.7+git20190123.241d060+dfsg-1)

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software 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.

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Architecture Package Size Installed Size Files
alpha (unofficial port) 192.4 kB748.0 kB [list of files]
amd64 189.1 kB630.0 kB [list of files]
arm64 167.4 kB578.0 kB [list of files]
armel 162.0 kB572.0 kB [list of files]
armhf 166.3 kB452.0 kB [list of files]
hppa (unofficial port) 184.3 kB613.0 kB [list of files]
i386 203.3 kB660.0 kB [list of files]
ia64 (unofficial port) 235.4 kB1,157.0 kB [list of files]
m68k (unofficial port) 185.6 kB648.0 kB [list of files]
mips64el 178.4 kB734.0 kB [list of files]
mipsel 178.8 kB733.0 kB [list of files]
ppc64 (unofficial port) 190.0 kB842.0 kB [list of files]
ppc64el 190.0 kB714.0 kB [list of files]
riscv64 (unofficial port) 185.3 kB536.0 kB [list of files]
s390x 171.7 kB626.0 kB [list of files]
sh4 (unofficial port) 217.9 kB602.0 kB [list of files]
sparc64 (unofficial port) 162.6 kB625.0 kB [list of files]
x32 (unofficial port) 189.2 kB596.0 kB [list of files]