Institut Pasteur blankvertical divider clipartblank C3BI blankvertical divider clipartblank Bioinformatics and Biostatistics Hub blankvertical divider clipartblank ALPS

ALPS ALPS

ALgorithmes et Programmation Scientifique

ALgorithmics and Programming in Science


Presentation

Welcome to the homepage of ALPS, one of the expert groups of the Bioinformatics and Biostatistics Hub from the C3BI, Institut Pasteur, Paris, France. ALPS group uses advanced computer skills in programming, algorithmics, visualization and software development to address issues of Pasteur’s teams by creating new software and methodologies. Developing scalable methods and visualizing results are a critical necessity in today’s research: ALPS group contribute to this goal by developing fast and efficient tools.

Institutional webpage

More details about ALPS (members, main projects, publication list): https://tinyurl.com/0-ALPS-1

Programs and Tools

Beautiful Pattern Matching (BPM) || a software for exact pattern matching of DNA
https://gitlab.pasteur.fr/ydufresne/bpm

Bioconvert || a collaborative project to facilitate the interconversion of life science data from one format to another Pypi Build Coverage Doc Install with
https://github.com/bioconvert/bioconvert

COMMET || a software providing a global similarity overview between all datasets of a large metagenomic project
https://github.com/pierrepeterlongo/commet

Compareads || a software designed to extract similar reads between huge metagenomic datasets
https://doi.org/10.1186/1471-2105-13-S19-S10

Counter RNAseq Window (CRAW) || a software to compute and visualize the coverage of RNA seq experiment Pypi Build Coverage Doc
https://gitlab.pasteur.fr/bneron/craw

IntegronFinder || a program that detects integrons in DNA sequences Build Doc
https://github.com/gem-pasteur/Integron_Finder

JASS || a python package that handles the computation of the joint statistics over sets of selected GWAS results, and the interactive exploration of the results through a web interface
https://research.pasteur.fr/en/software/jass-joint-analysis-of-gwas-summary-statistics/

Listeriomics || an Interactive Web Platform for Systems Biology of Listeria
https://listeriomics.pasteur.fr

MacSyFinder || a software providing a flexible framework to model the properties of molecular systems Doc
https://github.com/gem-pasteur/macsyfinder

MacSyView || an HTML5 interface to facilitate the analysis of results of the MacSyFinder tool
https://github.com/gem-pasteur/macsyview

Quality-aware fastq demultiplexer (qaf_demux) || a program demultiplexing fastq data having “in-line” barcodes
https://gitlab.pasteur.fr/bli/qaf_demux

Rapid Peptides Generator (RPG) || a software predicting proteases-induced cleavage sites on sequences Pypi Build Coverage Doc
https://gitlab.pasteur.fr/nmaillet/rpg

SHAMAN || a SHiny Application for Metagenomic ANalysis including the normalization, the differential analysis and multiple visualizations
http://shaman.c3bi.pasteur.fr/

SynTView || a comparative and interactive viewer for microbial genomes
http://genopole.pasteur.fr/SynTView

TXSScan || models and profiles for protein secretion systems (more informations)
https://galaxy.pasteur.fr/root?tool_id=toolshed.pasteur.fr%2Frepos%2Fodoppelt%2Ftxsscan%2FTXSScan%2F1.0.2
Download the protein profiles and the MacSyFinder models

Databases

MacSyDB/TXSSdb || a database of protein secretion systems in 1,528 complete genomes of bacteria with diderm-LPS cellular enveloppes. The models and profiles are to be used in conjunction with MacSyFinder and MacSyView
http://macsydb.web.pasteur.fr/txssdb/_design/txssdb/index.html

Miscellaneous

PasTeX || a beamer (LaTeX) template really close to the official Pasteur pptx theme
https://gitlab.pasteur.fr/nmaillet/PasTeX