Statistical Significance from Shuffles

 PRSS/PRFX compute the statistical significance of an alignment by aligning the two sequences, and then shuffling the second sequence 200 - 1000 times, and estimating the statistical significance from the distribution of shuffled alignment scores.

Window shuffles are used to preserve local sequence composition, e.g. for transmembrane proteins.

Search Databases with FASTA
Find Internal Duplications (lalign/plalign)

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

(A) Program: (B) Number of shuffles:
Uniform Window
(B.1) Enter first (query) sequence:  Subset range:
Entrez protein sequence browser

Entrez DNA 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 Get PSSM from NCBI Blast RID:
(C.1) Enter the second sequence:   Subset range:

(C.2) Or choose file of sequences/accessions:  
Other comparison options:
Scoring matrix:
 open:
 ext:
 Ktup:

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Copyright © 1988, 2006 by William R. Pearson and the University of Virginia. All rights reserved. The FASTA program and documentation may not be sold or incorporated into a commercial product, in whole or in part, without written consent of William R. Pearson and the University of Virginia.