:: DESCRIPTION
ShortFuse is a software to identify fusions with ambiguously mapping read pairs without generating numerous spurious fusions from the many mapping locations.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2011 Apr 15;27(8):1068-75. Epub 2011 Feb 16.
Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs.
Kinsella M, Harismendy O, Nakano M, Frazer KA, Bafna V.
:: DESCRIPTION
MitoDis is intended to implement a test to detect mitochondrial DNA mutation involvement.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Sun FZ, Cui J, Gavras H, and Schwartz F.
A Novel Class of Tests for the Detection of Mitochondrial DNA Mutation Involvement in Diseases.
Am. J. Hum. Genet. 72 (2003) pp. 1515-1526
:: DESCRIPTION
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.
::DEVELOPER
Apostolos Dimitromanolakis and Lei Sun
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hum Hered. 2002;54(2):99-110.
Enhanced pedigree error detection.
Sun L, Wilder K, McPeek MS.
:: DESCRIPTION
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.
:: DEVELOPER
Pieter De Bleser (VIB & Ghent University) & Bart Hooghe (VIB)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Genome Biol. 2007;8(5):R83.
A distance difference matrix approach to identifying transcription factors that regulate differential gene expression.
De Bleser P, Hooghe B, Vlieghe D, van Roy F.
:: DESCRIPTION
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.
::DEVELOPER
Institute for Advanced Biosciences
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Sugahara J, Yachie N, Sekine Y, Soma A, Matsui M, Tomita M, Kanai A. (2006).
SPLITS: a new program for predicting split and intron-containing tRNA genes at the genome level.
In Silico Biology. 6, 0039.
Sugahara J., Yachie N., Arakawa K., Tomita M. (2007)
In Silico Screening of Archaeal tRNA-encoding Genes Having Multiple Introns with Bulge-Helix-Bulge Splicing Motifs,
RNA; 13: 671-681
:: DESCRIPTION
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.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
M. Zytnicki, C. Gaspin, T. Schiex.
Darn – A Weighted Constraint Solver for RNA Motif Localization.
Constraints, Volume 13 (2008).
:: DESCRIPTION
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.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Woolfe, A., Mullikin, J., and Elnitski, L. 2009.
Genomic features defining exonic variants that modulate splicing.
Genome Biology. 11:R20
