Technical watch on structural bioinformatics

April 2013: Technical watch is a PF priority. On the 29th of april, the PF will contribute a course entitled "post-genomic era bioinformatics applied to structural biology" for the students of the IGBMC international PhD program. This is a wonderful opportunity to get a theoretical and practical overview on bioinformatics resources that may be helpful to structural biologists from whole genome sequencing to prediction of base substitution impact on protein structure and function. Noteworthy, the PF ensures the maintenance of valuable tools for integrative and comparative genomics such as PipeAlign (Plewniak, F. et al. 2003) (Ballast, DbClustal, Rascal, Leon, Clustering), Macsims, ARPAnno and EMBOSS . Swissprot, Trembl and the PDB (3D structures) databases which are maintained in SRS 8.3 will be updated once a month. All the previously mentioned softwares are accessible through web interface.

Laurent Bianchetti
Bioinformatics Platform of Strasbourg(BIPS)
Institute of Genetics and Molecular and Cellular Biology (IGBMC)
1 rue Laurent Fries, 67404 Illkirch, France

2013 Nucleic Acid Research (NAR) Database Issue is on-line

The 2013 NAR database issue publishes 176 articles, half of them present new database resources. In total, the molecular biology database collection currenty lists 1512 records. The information wealth of the database issue deserves an exhaustive read. In the light of recent publications at the IGBMC, 2 new databases of interspersed repetitive elements may be of particular interest, namely Dfam and SINEBase. The former uses hidden Markov models to annotate transposable elements in genomic DNA sequences, the latter has identified 175 families of SINE sequences in animal and plant organisms. Among previously recorded databases, HERVd classifies families of human endogeneous retroviruses.

Titles of the 176 articles published in NAR database issue (january 2013) NAR 2013 molecular biology database search engine

Publication

November 2012: In collaboration with Dr. Olivier Poch's laboratory of bioinformatics and integrative genomics (LBGI), the platform is pleased to announce a publication on transcriptional infidelity in cancer.

Pubmed link to abstract

Network of bioinformatics software users (RULBI)

The RULBI puts together biologists who use bioinformatics softwares under commercial licences (GeneSpring GX, Genomatix, NGS Avadis, and so on ...). Purchase request centralization at the national level enables the RULBI to negociate significantly reduced licence costs. Once a year, RULBI members gather to share experience on data analysis, attend presentations on new softwares and research projects which used RULBI identified tools that proved valuable to produce biological results and publications. The last RULBI meeting took place on the 29th March 2013 in the Curie Institute (Paris).