序列比对
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 asmultialign
andprofalign
, and visualize the alignment results in the序列比对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
序列比对 | 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.
- 序列比对s
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.