Compare Two Sequences

Compare two sequences aligns two sequences using the indicated algorithm, and calculates the statistical significance using shuffled sequences.

Near-optimal global alignments are also available here.

FASTA Program information

Search Databases with FASTA
Statistical Significance from Shuffles
Find Internal Duplications (lalign/plalign)

Choose: (A) program and (B, C) sequences to compare:

(A) Program:
(B.1) Enter first (query) sequence:  Subset range:
Annotate Query Sequence (SwissProt accessions)

Upload annotation file: 
Entrez protein / Entrez DNA sequence browser
Uniprot sequence browser
(B.2) Or upload sequence from file: 
Protein DNA (both-strands) DNA (forward only) DNA (rev-comp only)
Upload PSSM ASN.1 file: Help with PSSMs
(C.1) Enter the second sequence:   Subset range:
Annotate Target Sequence (SwissProt accessions)

Upload annotation file: 
          
Include isoforms
(C.2) Or choose file of sequences/accessions:  
Other comparison options:
Scoring matrix:
 open:
 ext:
 Ktup:
Output limits: Show Histogram
E(): Hide alignment
Hide Good Exons
Highlight:

FASTA program information | Download FASTA | About the Author

Copyright © 1996, 1997, 1998, 1999, 2002, 2014, 2015 by William R. Pearson and The Rector & Visitors of the University of Virginia
The FASTA package is open source software, licensed under the Apache License, Version 2.0 (the "License"); you may not copy this software except in compliance with the License. You may obtain a copy of the License at:
http://www.apache.org/licenses/LICENSE-2.0