www.gusucode.com > bioinfo 案例源码程序 matlab代码 > bioinfo/AlignMultipleSequencesExample.m
%% Align multiple sequences % This example shows how to align multiple protein sequences. % Copyright 2015 The MathWorks, Inc. %% % Use the |fastaread| function to read p53samples.txt, a FASTA-formatted file % included with Bioinformatics Toolbox(TM), which contains p53 protein % sequences of seven species. p53 = fastaread('p53samples.txt') %% % Compute the pairwise distances between each pair of sequences using % the 'GONNET' scoring matrix. dist = seqpdist(p53,'ScoringMatrix','GONNET'); %% % Build a phylogenetic tree using an unweighted average distance (UPGMA) % method. This tree will be used as a guiding tree in the next step of % progressive alignment. tree = seqlinkage(dist,'average',p53) %% % Perform progressive alignment using the PAM family scoring matrices. ma = multialign(p53,tree,'ScoringMatrix',... {'pam150','pam200','pam250'}) showalignment(ma)