PRALINE multiple sequence alignment

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For stable links, please refer to www.ibi.vu.nl/programs/ or www.ibi.vu.nl/programs/pralinewww/.

Our compute cluster is temporarily unavailable due to a major upgrade. We expect the server to be back online in the course of the next weeks (we hope before the end of May). We apologise for the inconvenience, and thank you for your continued patience.

♦ SOAP service ( 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:

Options

Exchange weights matrix: Associated gap penalties: BLOSUM62 PAM250 BLOSUM50 GON250 GON120  Help Open Extension  Help Progressive alignment strategy:  Help PSI-BLAST pre-profile processing (Homology-extended alignment)   PSI-BLAST Iterations 2 3 4 5 6 7 8 9 10 at an E-value cut-off of  DB NR Global pre-profile processing at a score cut-off of  Iterations 0 1 2 3 4 5 6 7 8 9 10 Standard progressive strategy Structural features:  Help   DSSP-defined secondary structure search YES  NO   Help   Secondary structure prediction No PSIPRED SSPRO PORTER YASPIN   Help   Transmembrane structure prediction No PHOBIUS TMHMM HMMTOP   Help Output customization:   Tree representation final alignment YES  NO   Help   Customize alignment colours YES  NO   Help   File format final alignment No file  MSF  FASTA   Help

E-mail

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