FastPairMI is a new software implementation for more efficiently computing the mutual information for all pairs of genes from gene expression microarrays.
Tomas Flouri, Kimon Frousios, Costas S. Iliopoulos, Kunsoo Park, Solon P. Pissis, and German Tischler. Approximate string-matching with a single gap for sequence alignment.
In Proceedings of the Second ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB 2011), pp. 490-492, 2011. ACM Digital Library
NW is an implementation of the Needleman and Wunsch dynamic programming sequence alignment algorithm. It reads PIR format sequence files and reports sequence similarity calculated in a number of different ways. Optionally it can generate a PIR format alignment file.
YAP (Yet Another Alignment Program) have the possibility of aligning two sequences of amino acids taking into account different properties, namely secondary structures, transmembranicity etc.
SNPduo is designed to provide an analysis of Single Nucleotide Polymorphism (SNP) data between any two individuals. It has been designed based on data exported from Affymetrix CNAT 4.0 or Illumina Beadstudio, as well as data downloaded from the HapMap project. However, provided that the data is formatted correctly SNPduoWeb can analyze any SNP data.
GS-Aligner that uses bit-level operations was developed for aligning genomic sequences. GS-Aligner is efficient in terms of both time and space for aligning two very long genomic sequences and for identifying genomic rearrangements such as translocations and inversions. It is suitable for aligning fairly divergent sequences such as human and mouse genomic sequences. It consists of several efficient components: bit-level coding, search for matching segments between the two sequences as alignment anchors, longest increasing subsequence (LIS), and optimal local alignment. Efforts have been made to reduce the execution time of the program to make it truly practical for aligning very long sequences. Empirical tests suggest that for relatively divergent sequences such as sequences from different mammalian orders or from a mammal and a nonmammalian vertebrate GS-Aligner performs better than existing methods.