Sequence Alignment

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

Functions

localalign Return local optimal and suboptimal alignments between two sequences
nwalign Globally align two sequences using Needleman-Wunsch algorithm
swalign Locally align two sequences using Smith-Waterman algorithm
seqdotplot Create dot plot of two sequences
seqpdist Calculate pairwise distance between sequences
seqalignviewer Visualize and edit multiple sequence alignment
multialign Align multiple sequences using progressive method
profalign Align two profiles using Needleman-Wunsch global alignment
seqconsensus Calculate consensus sequence
seqprofile Calculate sequence profile from set of multiply aligned sequences
seqlogo Display sequence logo for nucleotide or amino acid sequences
showalignment Display color-coded sequence alignment
hmmprofalign Align query sequence to profile using hidden Markov model alignment
hmmprofestimate Estimate profile hidden Markov model (HMM) parameters using pseudocounts
hmmprofgenerate Generate random sequence drawn from profile hidden Markov model (HMM)
hmmprofmerge Concatenate prealigned strings of several sequences to profile hidden Markov model (HMM)
hmmprofstruct Create or edit hidden Markov model (HMM) profile structure
showhmmprof Plot hidden Markov model (HMM) profile
blastlocal Perform search on local BLAST database to create BLAST report
blastncbi Create remote NCBI BLAST report request ID or link to NCBI BLAST report
blosum Return BLOSUM scoring matrix
dayhoff Return Dayhoff scoring matrix
gonnet Return Gonnet scoring matrix
nuc44 Return NUC44 scoring matrix for nucleotide sequences
pam Return Point Accepted Mutation (PAM) scoring matrix
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