The PROMALS multiple sequence alignment server

PROMALS constructs multiple protein sequence alignments using information from 
database searches and secondary structure prediction.     [Documentation]

News: try out our new program PROMALS3D, which automatically includes available
3D structural information.

Enter your sequences in FASTA format:                                                

Or upload a local file containing your sequences:
Enter your email address to receive the result (recommended):

Options for alignment parameters:
      -  Weight for amino acid scores:  
      -  Weight for predicted secondary structure scores:  
      -  Identity threshold above which fast alignment is applied:  

Options for running PSI-BLAST and processing of PSI-BLAST alignments:
      -  PSI-BLAST iteration number:  
      -  PSI-BLAST e-value inclusion threshold:  
      -  Identity cutoff below which distant homologs are removed:  
      -  Maximum number of homologs kept for PSI-BLAST alignment:  

Options for alignment output:
      -  Alignment block size:  
      -  Show conservation indices equal to or above:  
      -  Show starting and ending residue numbers:  
Enter a name for your job (recommended):          

PROMALS Documentation


Reference: PROMALS: towards accurate multiple sequence alignments of distantly related proteins. Jimin Pei and Nick V. Grishin. Bioinformatics 2007; doi: 10.1093/bioinformatics/btm017

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