ALICAO - Contact-based Sequence Alignment

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For stable links, please refer to www.ibi.vu.nl/programs/ or www.ibi.vu.nl/programs/alicaowww/index.php.

1. Template (single-chain structure) Enter PDB identifier of template: OR Upload single-chain template structure in PDB format: 2. Query (homologous sequence without structure) Upload (single) query sequence in FASTA format: 3. Options Help on Options 4.

ALICAO is a program to perform contact-based sequence alignment, where the structure of the first sequence is known (template) and the sequence of the second sequence is unknown (query). A contact map is extracted from the template structure and the program aligns the two sequences by maximizing a combination of contact mutation and sequence mutation probability. The combination of structure and sequence information overall improves alignments between sequences with < 30% sequence identity. For a more detailed description see Kleinjung et al. (2004) . The ALICAO program is available here . Please cite: J. Kleinjung, J. Romein, K. Lin and J. Heringa, Contact-based sequence alignment, Nucleic Acids Research 32(8) (2004) 2464-2473. bibtex

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The ALICAO server has been designed by Jens Kleinjung. Comments or problems to: jkleinj@cs.vu.nl

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