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Sequence Alignments

You can select from a list of analysis methods to compare nucleotide or amino acid sequences using pairwise or multiple sequence alignment functions.

Pairwise sequence alignment — Efficient 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 alignment — Functions for multiple sequence alignment (multialign, profalign) and functions that support multiple sequences (multialignread, fastaread, showalignment). There is also a graphical interface (seqalignviewer) for viewing the results of a multiple sequence alignment and manually making adjustment.

Multiple sequence profiles — Implementations for multiple alignment and 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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