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.

FASTA Program information

Search Databases with FASTA
Statistical Significance from Shuffles

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

(A) Program:
(B.1) Enter first (query) sequence:  Subset range:     Add termination codon
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)
(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:
     Output limits:
E():

Hide Alignments

FASTA program information | Download FASTA | About the Author

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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:
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