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PRALINE multiple sequence alignment


SOAP service (cog WSDL) now available.

PRALINE sample output

References and FAQs

PRALINE is a multiple sequence alignment program with many options to optimise the information for each of the input sequences; e.g. homology-extended alignment, predicted secondary structure and/or transmembrane structure information and iteration capabilities.

Paste in your PROTEIN sequences in FASTA format (MAX 500 sequences, length 2000):
Or upload a FASTA file (MAX 500 sequences, length 2000):
Enter a name for your job:
Exchange weights matrix:
Associated gap penalties:
 Help Open Extension  Help
Progressive alignment strategy:  Help
  PSI-BLAST Iterations at an E-value cut-off of  DB
at a score cut-off of  Iterations
Structural features:  Help
  DSSP-defined secondary structure search     Help
  Secondary structure prediction   Help
  Transmembrane structure prediction   Help
Output customization:
  Tree representation final alignment     Help
  Customize alignment colours     Help
  File format final alignment       Help
E-mail me when when my job is done at:

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