Compare Two Sequences

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

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: 
          
(C.2) Or choose file of sequences/accessions:  
Other comparison options:
Scoring matrix:
 open:
 ext:
 Ktup:
Output limits:
E():
Alignment Options: Highlight similarities differences compact differences.      Output format:

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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