Pairwise sequence alignment has received a new motivation due to the advent of recent patents in next-generation sequencing technologies, particularly so for the application of re-sequencing---the assembly of a genome directed by a reference sequence.
Finds genomic sequences that match a protein or DNA sequence submitted by the user. BLAT is a very fast sequence alignment tool similar to BLAST typically used for searching similar sequences within the same or closely related species. It was developed to align millions of expressed sequence tags and mouse whole-genome random reads to the human genome at a higher speed. BLAT is commonly used to look up the location of a sequence in the genome or determine the exon structure of an mRNA, but expert users can run large batch jobs and make internal parameter sensitivity changes by installing command line it on Linux server.
Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
Allows to attain efficiency adequate for aligning entire mammalian genomes and to increase its sensitivity. LASTZ is designed to preprocess one sequence or set of sequences and to align several query sequences to it. This tool works in several stages: (1) read sequence from target file, (2) infer scoring parameters, and (3) build a seed word position table for the target.
Manages and manipulates life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. It is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists. It provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project.
Compares two sequences looking for local sequence similarities. LALIGN produces k best “non-intersecting” local alignments for any chosen k. It needs only O(M + N + K) space, where M and N are the lengths of the given sequences and K is the total length of the computed alignments. The tool reports a number of non-overlapping alignments between sequences. LALIGN is a “linear-space algorithm” in the sense that it needs only space proportional to the sum of the input size and the output size.
Offers a framework for processing commonly used biological data. BioJava consists of several independent modules built using Maven. The software contains state-of-the-art algorithms, several file parsers, and data models to perform various calculations and to facilitate working with the standard data formats. It enables application development and analysis.