Posted on décembre 6, 2009 by admin
Next-generation sequencing
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MICSA
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A software for detecting transcription factor binding sites from NGS ChIPseq data
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SVdetect
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A software for detecting structural rearrangements from NGS mate-pair genomic sequencing data
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NG6
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Storage and basic analysis of data produced by the 454 sequencer of the Sequencing and Genotyping platform
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S-Mart
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Analysis tools box for high throughput management data: sequences produced by NGS technologies; for example, it manages RNA-Seq and ChIp-Seq data and provide many plots to visualize the data
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Genome annotation
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CAAT-Box
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Software package containing methods for the follow-up of the assembly phases and for initiating annotation during the finishing stage
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MicroScope/MaGe
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(Re)annotation and comparative analysis of microbial genomes
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Rasta-Bacteria
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Rapid Automated Scan for Toxins and Antitoxins in Bacteria
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AGMIAL
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Integrated system for bacterial genome annotation
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Genome visualisation
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SynteBase/SynteView
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A tool to visualize gene order conservation in prokaryotic genomes
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Autograph
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Interactive web server for automating and visualizing comparative genome maps
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MuGeN
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Software package for the visual exploration of multiple annotated genome portions
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DNA & Protein motifs
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Dr Motifs
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A comprehensive portal for pattern matching and discovery.
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STAN
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Nucleic or proteic pattern search based on SVG (String Variable Grammar)
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CRISPI
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User-friendly web interface with many graphical tools and facilities allows extracting CRISPR, finding out CRISPR in personal sequences or calculating sequence similarity with spacers
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ModuleOrganizer
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Detecting modules in families of transposable elements
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Hectar
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Heterokont subcellular targeting prediction (ABiMS resource)
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R’MES
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Finding exceptional motifs in sequences
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PRIAM
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Enzyme-specific profiles for metabolic annotation
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REPET
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Analysis tool for detection, annotation and analysis of repeats in genomic sequences, specifically designed for transposable elements (TEs)
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BLASTER
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Analysis suite for transposable element search and annotation in large eukaryotic genome sequence but generic enough to be applied in other contexts
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RNA
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VARNA
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Interactive drawing and editing of the RNA secondary structure
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Erpin
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A program for the detection of RNA motifs inferred from RNA sequence alignments
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RNAspace
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Integrated environment for non-coding RNA annotation; RNAspace makes available a variety of ncRNA gene finders and ncRNA databases as well as user-friendly tools to explore computed results including comparison, visualization and edition of putative RNAs
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Phylogeny
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PhyML
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A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
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TreeDyn
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Dynamic graphics and annotations for analyses of trees
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GenePop
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Population genetics software package
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APE
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Analyses of phylogenetics and evolution in R language
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MLVA web service
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Databases of tandem repeats typing data for population studies of bacterial pathogens; tools to produce additional private or public databases
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Phylogeny.fr
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Automated and configurable workflow for molecular phylogeny
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SeaView
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Multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny
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Miscellaneous
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GenRGenS
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Software for generating random genomic sequences and structures
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genofrag/iThos
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Tool for segmenting bacterial genomes into fragments of identical size for long-range PCR amplification
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Gigablaster
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Fast parallel Blast search on specialized sequence databases
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Tcoffee
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A collection of tools for computing, evaluating and manipulating multiple alignments of DNA, RNA, protein sequences and structures
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ADE-4
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Software package for multivariate statistics, official R package since 2002
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DICROPROT
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Analysis of circular dichroism spectra
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AnTheProt
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Graphical user interface for protein sequence analysis and molecular graphic display (Windows systems)
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