ShortFuse is a software to identify fusions with ambiguously mapping read pairs without generating numerous spurious fusions from the many mapping locations.
Prest-plus (Pedigree RElationship Statistical Test) is a software packages for detection of pedigree errors, cryptic relatedness and relationship mispecification in GWAS or linkage data. Using an optimized MLE estimator for IBD probabilities, prest-plus computes accurate estimates for IBD0/1/2 using any number and combination of SNP or microsatellite marker data. It can work as efficiently and accurately with a microsatellite linkage panel or SNP data from a GWAS study.
TFdiff identifies the context-dependent transcription factor binding sites (TFBSs) interactions that may yield an explanation why the expression of genes is modified in different directions given a particular condition.
SPLITS and SPLITSX, expansion programs for tRNAscan-SE to detect spliced-tRNA genes, such as split-tRNA genes (Figure A) and intron-containing tRNA genes (Figure B) in archaea.
The length of the query sequence should be limited within 5 mega base pairs (nucleotide). If your sequence is longer than this, please divide the sequence and submit separately. Finally these programs are under active development. If you use these programs, please help me out by e-mailing me with suggestions, comments, and bug reports.
Darn is a RNA motif search tool. It finds all the subsequences that match a specified motif on some input genomic sequence(s).Darn uses a weighted constraint solver to localize the portions of a genomic sequence that match a motif. The motif is expressed in a specific language (see section 5). Some motif descriptors are provided with the software for FMN, Lysine, RNaseP, SAM,snoRNA C/D-box and tRNA search.
Skippy is a Web-based tool that allows users to input a set of exonic variants to score them for a number of features (such as changes in splicing regulatory elements) that have been shown to be predictive of known genome variations that cause exon skipping or activation of ectopic splice sites. In this way, variants can be either prioritized for further splicing-based functional analysis or the results can be used as further genomic evidence in cases in which the causative variant is already known.