Sequence Alignment
Multiple, pairwise, and profile sequence alignments using dynamic
programming algorithms; BLAST searches and alignments; standard and
custom scoring matrices
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
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.
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.
