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.

FASTA Program information

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:
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:

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