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/.

♦ 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

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