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 Alignment | Visualize and edit multiple sequence alignments |
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 |
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.
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.