SECISaln 1.0 Web Server 2008

SECISaln will predict a eukaryotic SECIS element in a nucleotide sequence, split it into its structural units and then align each unit against the SECISes in our database. SECISaln can distiguish between typeI and typeII SECIS elements and will align the submitted sequence against others of the same type. All sequences used by SECISaln have been collected from either GenBank or EGO

SECISaln is not intended to replace SECISearch as a SECIS element predictor. In fact, SECISaln uses SECISearch to predict SECIS elements. The objective of this tool is to provide researchers with an easy way to compare structural features of SECIS elements. It should only be used on sequences known to contain a SECIS element. The pattern used by SECISaln to recognise SECIS elements is very permissive and would result in false positives when run on unknown sequences.

Pattern: Search complementary strand.
Overall structure energy
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Credits: SECISaln uses SECISearch, PatScan and RNAfold from the Vienna RNA Package.

If you find this software useful please cite Chapple C. E. et al, Bioinformatics, 2009 25(5):674-675

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Please send questions and comments to charles.chapple AT crg DOT es