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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

Apps

Sequence AlignmentVisualize and edit multiple sequence alignments

Functions

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
seqdotplotCreate dot plot of two sequences
seqpdistCalculate pairwise distance between sequences
seqalignviewerVisualize and edit multiple sequence alignment
multialignAlign multiple sequences using progressive method
profalignAlign two profiles using Needleman-Wunsch global alignment
seqconsensusCalculate consensus sequence
seqprofileCalculate sequence profile from set of multiply aligned sequences
seqlogoDisplay sequence logo for nucleotide or amino acid sequences
showalignmentDisplay color-coded sequence alignment
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
blastlocalPerform search on local BLAST database to create BLAST report
blastncbiCreate remote NCBI BLAST report request ID or link to NCBI BLAST report
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

Examples and How To

Compare Sequences Using Sequence Alignment Algorithms

Starting with a DNA sequence for a human gene, locate and verify a corresponding gene in a model organism.

View and Align Multiple Sequences

Use the Sequence Alignment app to visually inspect a multiple alignment and make manual adjustments.

Concepts

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.

Sequence Utilities and Statistics

You can manipulate and analyze your sequences to gain a deeper understanding of the physical, chemical, and biological characteristics of your data.

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