Project-sequoia:Carnac – RNA structure prediction

Team sequoia

Members

Overall Objectives

Highlights of the year
Objectives

Scientific Foundations

Introduction
Sequence processing and Next Generation Sequencing
Comparative analysis and Noncoding RNAs
Non ribosomal peptides synthesis
High-performance bioinformatics

Software

Introduction
YASS – local homology search
Carnac – RNA structure prediction
Gardenia – RNA structure alignment
Regliss – RNA locally optimal structures
Protea – coding sequence identification
Magnolia – multiple alignment via comparative analysis
CG-seq – comparative genomics
RNAspace – a platform for noncoding RNA annotation
Norine – a resource for nonribosomal peptides

New Results

Sequence processing and Next-Generation Sequencing
Protein coding sequences
Comparative analysis and Noncoding RNAs
Non ribosomal peptides synthesis
High-performance bioinformatics
Genome rearrangements

Contracts and Grants with Industry

NVIDIA

Other Grants and Activities

Regional initiatives and cooperations
National initiatives and cooperations
International initiatives and cooperations

Dissemination

Organization of workshops and seminars
Editorial and reviewing activities
Miscellaneous activities
Meetings attended and talks
Teaching activities
Administrative activities

Bibliography

Major publications
Publications of the year
References in notes

Inria / Raweb 2009
Presentation of the Project sequoia

Section: Software

Carnac – RNA structure prediction

The caRNAc program implements our idea for RNA structure prediction presented in Section 3.3 . It is written in C and is distributed under the Cecill license. The web interface offers 2D visualisation tools with Naview and alignment functionalities. It has proven to be very fast and very specific compared to its competitors.

Logo Inria