Multiple Sequence Alignment Tools for KYG
version 1.1
Three steps for building the alignment for the prediction of RNA interface residues
1. Convert PDB to FASTA format, 2. Make input sequence file in FASTA format, and 3. upload the file to align
  1. Upload the PDB file you want to predict and extract aa sequence from ATOM lines.
    PDB file only:

  2. Make a single input sequence file with the output #1 and homologous sequences at hand.

  3. Upload the FASTA format sequence file and run the alignment tool. The result will sooner (or later) appears on the screen.
    FASTA format amino acid sequence only:
    Note 0: Be patient. The alignment sometimes takes some time.
    Note 1: Due to the limitaiton of computational power, the number of whole amino acid residues is limited to 50,000.
    Note 2: To save computational time, trim the sequences to the relevant domain.

  4. Save the sequence in a file as is and upload the alignment for the RNA-binding residue prediction.
update: 30th, Dec., 2008
Copyright(c) 2008, Laboratory of Computational Biology, Ochanomizu University, All Rights Reserved.