| Bioinformatics Toolbox | |
You can select from a list of analysis methods to perform pairwise or multiple sequence alignment.
Pairwise sequence alignment — The toolbox provides efficient MATLAB implementations of standard algorithms such as the Needleman-Wunsch (nwalign) and Smith-Waterman (swalign) algorithms for pairwise sequence alignment. The toolbox also includes standard scoring matrices such as the PAM and BLOSUM families of matrices (blosum, dayhoff, gonnet, nuc44, pam). Visualize sequence similarities with seqdotplot and sequence alignment results with showalignment.
Multiple sequence profiles — The toolbox provides MATLAB implementations for profile hidden Markov model algorithms (gethmmprof, gethmmalignment, gethmmtree, pfamhmmread, hmmprofalign, hmmprofestimate, hmmprofgenerate, hmmprofmerge, hmmprofstruct, showhmmprof).
Biological codes — Look up the letters or numeric equivalents for commonly used biological codes (aminolookup, baselookup, geneticcode, revgeneticcode).
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