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.

Apps

Sequence Alignment

Visualize and edit multiple sequence alignments

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

`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`	Displays a set of HMM profile alignments
`hmmprofstruct`	Create or edit hidden Markov model (HMM) profile structure
`showhmmprof`	Plot hidden Markov model (HMM) profile

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

Topics

Compare Sequences Using Sequence Alignment Algorithms
Determining the similarity between two sequences is a common task in computational biology.
View and Align Multiple Sequences
Use the Sequence Alignment app to visually inspect a multiple alignment and make manual adjustments.
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.