Description: SynaMine is an application which identifies potentially novel "regions of importance" in nucleotide or protein sequences by scoring the predictability of patterns stored in a SynaBASE. No other algorithmic or predictive approaches are necessary to obtain results.

Application Example: Using a protein SynaBASE and a nucleotide sequence, the nucleotide-protein mining of the sequence reveals areas which potentially encode genic regions.

Human cDNA clone BU185479.1 was queried against a SynaBASE of SwissProt using SynaMine. Queries against SynaMine are typically returned within 200 milliseconds.

With the assumption that the gene is translated, the SynaMine result indicates sections in several frames of the gene that may encode for protein domains or motifs.

Detailed analysis of keywords suggests gene function based upon inference from predictability of patterns using SwissProt data. In addition to matching these known regions, additional new keywords are identified, which may suggest potential new novel regions or domains. In this example, the annotation suggests a role as a monoglyceride lipase, but SynaMine also suggest roles as a hydrolase, lipase, esterase or monoglyceride.

To try SynaMine please:

1. Click here and then click on the "Access Now" button
2. Click on SynaMine
3. Paste the sequence below into the SynaMine application and click the "Mine" button
4. Once you have the results you can click and drag a region to review the keyword annotations.

Note: query size limits for free unregistered users are set to a maximum of 2Kbp

>gi|22699463|gb|BU185479.1|BU185479 AGENCOURT_8042914 NIH_MGC_110 Homo sapiens cDNA clone IMAGE:6084411 5', mRNA sequence
CGTCCCGGCCCTGGCCCGCCGCAAACGAGGATCCGCTGCGCTCGGGGAACGCGACAGCGGCGCTCGTGGCCCCGGACCTGAAGACCCTTCCAGCATGCCAGAGGA AAGTTCCCCCAGGCGGACCCCGCAGAGCATTCCCTACCAGGACCTCCCTCACCTGGTCAATGCAGACGGACAGTACCTCTTCTGCAGGTACTGGAAACCCACAGG CACACCCAAGGCCCTCATCTTTGTGTCCCATGGAGCCGGAGAGCACAGTGGCCGCTATGAAGAGCTGGCTCGGATGCTGATGGGGCTGGACCTGCTGGTGTTCGC CCACGACCATGTTGGCCACGGACAGAGCGAAGGGGAGAGGATGGTAGTGTCTGACTTCCACGTTTTCGTCAGGGATGTGTTGCAGCATGTGGATTCCATGCAGAA AGACTACCCTGGGCTTCCTGTCTTCCTTCTGGGCCACTCCATGGGAGGCGCCATCGCCATCCTCACGGCCGCAGAGAGGCCGGGCCACTTCGCCGGCATGGTACT CATTTCGCCTCTGGTTCTTGCCAATCCTGAATCTGCAACAACTTTCAAGGTCCTTGCTGCGAAAGTGCTCAACCTTGTGCTGCCAAACTTGTCCCTCGGGCCCAT CGACTCCAGCGTGCTCTCTCGGAATAAGACAGAGGTCGACATTTATAACTCAGACCCCCTGATCTGCCGGGCAGGGCTGAAGGGGTGCTTCGGCATCCAACTGCT GAATGCCGTCTCACGGGTGGAACGCGCCCCTCCCCAAGCTGACTGGGCCCTTCCTGCTGCTCCGGGGCTCTGCCGGATCGCCTATGTGACAGCAAAGGGGGCCTA CCTGGCTCATGGGGTTTAGCCCAGAGGCCCGGAAAA