Find Internal Duplications (lalign/plalign)

 LALIGN/PLALIGN find internal duplications by calculating non-intersecting local alignments of protein or DNA sequences. LALIGN shows the alignments and similarity scores, while PLALIGN presents a "dot-plot" like graph.
Search Databases with FASTA
Statistical Significance from Shuffles

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

(A) Program: Show identity alignment
(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)
(C.1) Enter the second sequence:   Subset range:

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

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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.