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Sequence Alignment

Multiple, pairwise, and profile sequence alignments using dynamic programming algorithms; BLAST searches and alignments; standard and custom scoring matrices

Compare nucleotide or amino acid sequences using pairwise or multiple sequence alignment functions. Standard algorithms for pairwise alignments include Needleman-Wunsch (nwalign) and Smith-Waterman (swalign) algorithms. You can also perform multiple sequence alignment using various functions, such as multialign and profalign, and visualize the alignment results in the Sequence Alignment app. In addition, you can use a hidden Markov model (HMM) to align a query sequence to an HMM profile. Perform BLAST searches against known sequences in online databases using various BLAST programs.


Sequence AlignmentVisualize and edit multiple sequence alignments


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localalignReturn local optimal and suboptimal alignments between two sequences
nwalignGlobally align two sequences using Needleman-Wunsch algorithm
swalignLocally align two sequences using Smith-Waterman algorithm
multialignAlign multiple sequences using progressive method
profalignAlign two profiles using Needleman-Wunsch global alignment
seqdotplotCreate dot plot of two sequences
seqpdistCalculate pairwise distance between sequences
seqalignviewerVisualize and edit multiple sequence alignment
seqconsensusCalculate consensus sequence
seqprofileCalculate sequence profile from set of multiply aligned sequences
seqlogoDisplay sequence logo for nucleotide or amino acid sequences
hmmprofalignAlign query sequence to profile using hidden Markov model alignment
hmmprofestimateEstimate profile hidden Markov model (HMM) parameters using pseudocounts
hmmprofgenerateGenerate random sequence drawn from profile hidden Markov model (HMM)
hmmprofmergeDisplays a set of HMM profile alignments
hmmprofstructCreate or edit hidden Markov model (HMM) profile structure
showhmmprofPlot hidden Markov model (HMM) profile
blosumReturn BLOSUM scoring matrix
dayhoffReturn Dayhoff scoring matrix
gonnetReturn Gonnet scoring matrix
nuc44Return NUC44 scoring matrix for nucleotide sequences
pamReturn Point Accepted Mutation (PAM) scoring matrix
blastncbiCreate remote NCBI BLAST report request ID or link to NCBI BLAST report