Sequence Alignment
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 |
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.