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We would like to be able to use IgBlast on the Galaxy platform. We are studying B cells in adaptive immune response, and are particularly interested in the antibodies termed as broadly neutralizing antibodies (bNAbs). By definition, these antibodies can neutralize most known HIV-1 strains, and are produced by rare infected individuals several years post-infection. We are currently investigating the bNabs immunoglobulin repertoire by focusing our NGS (454 pyrosequencing) analysis on immunoglobulin sequences (V-domains) from HIV-infected patients who developed bNAbs. As immunoglobulin sequences result from the combinatorial rearrangement of 3 gene segments : V , (D) and J gene segments, we need a specific tool to analyze these sequences. Indentifying the germline genes which are involved in the rearrangment is an essential step. Two main tools are being widely used to analyze Immunoglobulins: IMGT and IgBlast. IgBlast has several advantages; it is based on BLAST (it is then possible for the user to build his own database), open source, can use protein or nucleotide sequences as input, and most of all, IgBlast is already installed on the Institut Pasteur's cluster as well as the germline genes database. As it would be very convenient for us to use the bic cluster and galaxy platform to run our analyzes, we would be grateful if IgBlast could be implemented in the Pasteur Galaxy Platform. In this regard, we are of course fully disposed to help in any ways. We also believe that it would be very useful to people working on immunoglobulin sequences in the immunology department by building specific pipelines. Thank you very much.
PhageTermini: a Fast and User-friendly Software to Determine Bacteriophage Packaging Mode and Termini
The PhageTermini software was developed to allow biologists acquire valuable information on bacteriophage termini sequences and packaging mode using phage sequenced with the Illumina TruSeq technology.
Development of a web application and new functionalities for the maintenance and curation of iPPI-DB
A new version of the iPPI-DB, a manually curated database that contains the structure, some physicochemical characteristics, the pharmacological data and the profile of the PPI targets of several hundred modulators of protein-protein interactions.
This new version will include:
- A maintenance application that facilitates and automates the updates of the database. The computation of the various physico-chemical properties of the modulators and chemical similarity screening on the Galaxy server of the Institut Pasteur.
- A new target-centric mode, based on the mapping of all druggable cavities at the core of PPI interfaces throughout the Protein Data Bank.
The ARIA (Ambiguous Restraints for Iterative Assignment) software, developed at the Structural Bioinformatics Unit, automatizes the treatment of NMR data and protein structure calculation by molecular dynamics simulation. To enhance the visibility of the software, it is necessary to develop a new web interface where users will be able to easily manage their data, perform calculations and analyze the results of the ARIA calculations.
Mosquitoes of the Anopheles gambiae complex display strong preference for human blood- meals and are major malaria vectors in Africa. However, their interaction with viruses or role in arbovirus transmission during epidemics has been little examined, with the exception of O’nyong-nyong virus, closely related to Chikungunya virus. We have recently identified two novel insect RNA viruses, a Dicistrovirus and a Cypovirus, found in laboratory colonies of An. gambiae taxa using small-RNA deep sequencing. Wild-collected Anopheles from Senegal and Cambodia were positive for the Dicistrovirus and Cypovirus, displaying high sequence identity to the laboratory-derived virus. Thus, the Dicistrovirus (Anopheles C virus, AnCV) and Cypovirus (Anopheles Cypovirus, AnCPV) are components of the natural virome of at least some anopheline species. We purified the AnCPV virus by propagation on a insect cell line and we amplified and sequenced RNA extracted from the cellular supernatent. Our goal is to completely sequence the AnCPV, a dsRNA virus with an segmented genome.
The APOBEC3 proteins (APOBEC3A-H) are single-stranded DNA (ssDNA) cytidine deaminases (CDAs). Those proteins were first tied to innate immunity as antiviral restriction factors as cytidine deamination to uridine results in hypermutation of viral genomes. However APOBEC3 mutațional signature was recently identified in cancer genomes, suggesting a causal role of APOBEC3 proteins in cancer onset. Accordingly, we demonstrated that both APOBEC3A and APOEC3B proteins can elicit somatic mutations on chromosomal DNA. The aim of this project is to implement in Pasteur's Galaxy Instance the MutSpec Tool box, allowing the analysis of mutational signature from cancer genomes. This tool will allow to seek and extract APOBEC3 mutational signatures from genomes available in public databases such as TCGA or COSMIC. This tool is also a prerequiste to start implementing NGS sequencing in the lab's forthcoming work.