MAGIIC-PRO employs a novel combination of intra- and inter-block gap constraints to discover functional long motifs that are interleaved by several large irregular gaps. more... on the feature of MAGIIC-PRO and the comparison to related works.

ˇ§Please notice that the citation numbers (from 5 to 23) in our paper are terribly wrong due to some unexpected event happened in the final stage of proof reading. NAR is currently arranging for a corrigendum and that will be published soon. Each number (from 5 to 23) must be decreased by 1.ˇ¨
You have four ways to prepare training data for discovering long patterns
1. Use PSI-BLAST to find homologues for a query protein
In this way, you should have either a Swiss-Prot accession number or a query sequence in FASTA format

OR
2. Exploit Swiss-Prot cross-reference annotation
In this way, you should have the Swiss-Prot accession number for the query protein

OR
3. Prepare the training data by secondary database ID
In this way, the first sequence will be assigned as the reference protein

OR
4. Prepare the training data by 'copy and paste'
In this way, you should have the set of protein sequences

For any questions or suggestions please contact Chen-Ming Hsu .
If you find MAGIIC-PRO useful, please kindly cite:
Hsu CM, Chen CY, and Liu BJ, MAGIIC-PRO: Detecting functional signatures by efficient discovery of long patterns in protein sequences. Nucleic Acids Research 2006, 34:W356-W361.
 This site was last updated on Sat., July 1 2006.

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