V-Xtractor is a Perl-based, high-throughput software tool that locates, verifies, and extracts defined segments of sequence information from sequence datasets. Hidden Markov Models are used to detect the conserved boundaries of the target region and to extract the interjacent sequence information (that is for example the hyper-variable regions of the rRNA gene or the internal transcribed spacer regions of the rRNA operon). This tool extracts phylogenetically comparable regions without prior multiple sequence alignments and improves reliability of the data by confirming basic authenticity of the sequence.
EDGE is a software package for the significance analysis of DNA microarray experiments for both standard and time course experiments based on our new Optimal Discovery Procedure and Time Course Methodology
ACME (Advanced parallel motif extractor) is an advanced parallel motif extractor. ACME arranges the search space in contiguous blocks that take advantage of the cache hierarchy in modern architectures, and achieves almost an order of magnitude performance gain in serial execution.
XSTREAM is a rapid and powerful algorithm for identifying perfect and degenerate tandem repeat motifs in protein (and nucleotide) sequence data. XSTREAM also effectively models the architecture of repetitive domains in tandem repeat proteins and eliminates motif redundancy to identify “fundamental” tandem repeat patterns.
Solon P. Pissis, Alexandros Stamatakis, and Pavlos Pavlides.
MoTeX: a word-based HPC tool for MoTif eXtraction.
the Fourth ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB 2013), pp. 13-22, 2013. ACM Digital Library