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Software to cluster protein sequences into functionally similar groups. Journal reference: http://bioinformatics.oxfordjournals.org/cgi/content/short/24/16/1765
AnnaF is an automatic gene annotation framework, that is used to do some automatic annotation for C. higginsianum. It was also tested on F. graminearum and should work well for fungi in general.
AnnaF was build upon the pipeline framework Anna.
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* Java classes for parsing text, conversion to XML or to evaluate in Java. The parser is textual-script-controlled with a syntax near Backus Naur Format, named ZBNF. * Some routines for conversion: C-Header or Java to XMI, XML-Documentation generation,
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LAITOR is a text mining software developed to find co-occurrence of biological entities (gene/protein terms) together with biointeractions and concepts term from customized dictionaries.
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Snap (snap-pari) is a computer program for studying arithmetic invariants of hyperbolic 3-manifolds. See: Computing arithmetic invariants of 3-manifolds by Coulson, Goodman, Hodgson and Neumann, Experimental Mathematics Vol.9 (2000) 1.
RADAR stands for Rapid Automatic Detection and Alignment of Repeats in protein sequences. RADAR identifies gapped approximate repeats and complex repeat architectures involving many different types of repeats.
Radar has moved to github (https://github.com/AndreasHeger/radar)
BARNACLE is a Python library for RNA 3D structure prediction. It can be used for probabilistic sampling of RNA structures that are compatible with a given nucleotide sequence and that are RNA like on a local length scale.
A cross-platform library that computes fast and accurate SIFT image features. libsiftfast provides Octave/Matlab scripts, a commandline interface, and a python interface (siftfastpy). Optimized with SIMD instructions and OpenMP .
dprimer is a commandline utility for designing degenerate PCR primers against multiple, aligned sequences. Its primary use case is searching for a family of related pathogens in a host tissue sample.
Maximally flat (maxflat) digital filter design in Java, with arbitrary numbers of poles and zeros. "Maximally flat" means that the magnitude frequency response has the maximum number of vanishing derivatives at 0 and pi.
On December 8, 2009 the UK Met Office released records of worldwide land surface temperature readings. This project analyzes these records and produces output files that can be read by gnuplot and Google Earth to show temperature trends.
LIGR Assembler is a sequence assembly program. It was derived from TIGR Assembler and addresses some of TIGR Assembler's shortcomings. See the CHANGES file for details.
Converts Digital Terrain Elevation Data from one level to another. (Currently only converts DTED1>DTED2) No longer in development due to personal time constraints. If there are features you desperately need, feel free to ask, or write it your self :)
This is a reference implementation of snoBAC, a Bayesian Classifier designed to predict box H/ACA snoRNAs in Caenorhabditis nematode genomes. For details of algorithm and data, see Wang and Ruvinsky (2009) RNA in press.
Avenzoar is a one-year exploration of renal cell carcinoma morphology and its related single nucleotide polymorphisms (SNPa) as a method of automating diagnosis of cancer by using a computer-aided decision tree controlled by analytical statistics.
The aim of project is creating program environment for solving some integral equations, arising at solving mathematical problems of the diffraction theory.