SIC (Scan Inverse Complementary)

The aim of SIC is to detect segments which are likely inverted in a sequence.

The web software SIC provides a tool to search short inverted segments (length 3 Bp to 5000 Bp) in a DNA sequence. The sequence is assumed to follow a Markov model. Searching inverted segment is done by a scan approach after you specify the size of the scanning window and the order of the Markov chain. A list of the highest score segments is given with an assessment of the randomness of the result.

Access SIC on the WEB

Download SIC for a local installation (Documentation)

Consult the results on Bacterial Genome (via SHIBA)


SHIBA (SHort Inversions in BActeria)

SIC was extensively run on all the complete genomes of bacteria present on the NCBI server to the date of september 2005. Long genomes were arbitrarily split into pieces of 20000 bases pairs long in order to compensate the heterogeneity of the nucleotides composition along the complete sequence. You can also consult the results stored on the SHIBA database.

References :

SIC: a tool to detect short inverted segments in a biological sequence, David Robelin, Hugues Richard and Bernard Prum, Nucleic Acids Research, 2003, Vol. 31, No. 13 3669-3671

Detecting short inverted segments in a biological sequence, David Robelin, Bernard Prum, proceedings of the European Conference on Computational Biology, Paris, 2003

What's new ?

15/11/2005 - Birth of the database SHIBA which contains the results of the detection of short inverted segments by SIC in complete bacterial genomes. The detected segments are linked with their known annotations and their context.
17/11/2004 - The new WEB service is on with more convivial interface.
16/08/2004 - Good news : SIC will profit from a beautiful and powerful new server.
- Bad news : The server is not ready yet, and we should wait to delight in it.
04/12/2003 - Bug correction in the score method of SIC.
28/11/2003 - NEW : The version 1.1 of SIC can be downloaded for a local installation on Linux/unix type system. In this version, in it is not necessary to fix a priori the size of the returned segments. Some Bugs were also corrected form the previous version.
17/11/2003 - The version 0.1 of SIC can be downloaded for a local installation on Linux/unix type system. It requires the GSL library (Gnu Scientific Library).
10/09/2003 - The server had problems during 2 weeks of september and August. Apologies for this. The bug is fixed now.
David Robelin
Last modified: Fri Mar 31 13:56:05 CEST 2006