Software
I am involved in the design, implementation, maintenance, and usage of many production-level (bioinformatics) tools. Some of them are listed below:
- CNEFinder:
A tool for identifying conserved non-codings elements (CNEs) between two given DNA sequences with user-defined criteria.
CNEFinder does not require or compute whole-genome alignments or indexes, such as the suffix array or the Burrows Wheeler Transform (BWT), which makes it flexible to use on a wide scale.
- MoTeX:
A word-based high-performance computing tool for MoTif eXtraction.
MoTeX is an accurate and efficient tool for single and structured MoTif eXtraction.
It comes in three flavors: the standard CPU version; the OpenMP-based version; and the MPI-based version.
It includes a tool that implements measures for assesing the statistical significance of the reported motifs.
- MARS:
MARS is a program, which can be used in conjunction with any multiple sequence alignment program, to improve
Multiple circular sequence Alignment using Refined Sequences. Typical input sequences include mitochondrial DNA, viroid, viral or other circular genomes.
- MAW:
A software suite on the computation and application of Minimal Absent Words.
MAW includes among others the fastest (to the best of our knowledge) implementation for computing MAWs in intenal memory, an
OpenMP implementation for computing MAWs, and an implementation for computing MAWs in
external memory.
- REAL:
An efficient short REad ALigner for next-generation sequencing reads.
REAL was designed in 2009 for short Illumina/Solexa reads.
To the best of our knowledge, it still remains one of the fastest and more accurate tools for this purpose.
See here for a benchmark.