Archive for the Genomics Category

Sequence analysis tools

Posted on décembre 6, 2009 by Commentaires fermés sur Sequence analysis tools

Next-generation sequencing

MICSA A software for detecting transcription factor binding sites from NGS ChIPseq data
SVdetect A software for detecting structural rearrangements from NGS mate-pair genomic sequencing data
NG6 Storage and basic analysis of data produced by the 454 sequencer of the Sequencing and Genotyping platform
S-Mart 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

Genome annotation

CAAT-Box Software package containing methods for the follow-up of the assembly phases and for initiating annotation during the finishing stage
MicroScope/MaGe (Re)annotation and comparative analysis of microbial genomes
Rasta-Bacteria Rapid Automated Scan for Toxins and Antitoxins in Bacteria
AGMIAL Integrated system for bacterial genome annotation

Genome visualisation

SynteBase/SynteView A tool to visualize gene order conservation in prokaryotic genomes
Autograph Interactive web server for automating and visualizing comparative genome maps
MuGeN Software package for the visual exploration of multiple annotated genome portions

DNA & Protein motifs

Dr Motifs A comprehensive portal for pattern matching and discovery.
STAN Nucleic or proteic pattern search based on SVG (String Variable Grammar)
CRISPI 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
ModuleOrganizer Detecting modules in families of transposable elements
Hectar Heterokont subcellular targeting prediction (ABiMS resource)
R’MES Finding exceptional motifs in sequences
PRIAM Enzyme-specific profiles for metabolic annotation
REPET Analysis tool for detection, annotation and analysis of repeats in genomic sequences, specifically designed for transposable elements (TEs)
BLASTER Analysis suite for transposable element search and annotation in large eukaryotic genome sequence but generic enough to be applied in other contexts

RNA

VARNA Interactive drawing and editing of the RNA secondary structure
Erpin A program for the detection of RNA motifs inferred from RNA sequence alignments
RNAspace 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

Phylogeny

PhyML A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
TreeDyn Dynamic graphics and annotations for analyses of trees
GenePop Population genetics software package
APE Analyses of phylogenetics and evolution in R language
MLVA web service Databases of tandem repeats typing data for population studies of bacterial pathogens; tools to produce additional private or public databases
Phylogeny.fr Automated and configurable workflow for molecular phylogeny
SeaView Multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny

Miscellaneous

GenRGenS Software for generating random genomic sequences and structures
genofrag/iThos Tool for segmenting bacterial genomes into fragments of identical size for long-range PCR amplification
Gigablaster Fast parallel Blast search on specialized sequence databases
Tcoffee A collection of tools for computing, evaluating and manipulating multiple alignments of DNA, RNA, protein sequences and structures
ADE-4 Software package for multivariate statistics, official R package since 2002
DICROPROT Analysis of circular dichroism spectra
AnTheProt Graphical user interface for protein sequence analysis and molecular graphic display (Windows systems)

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Filed Under: Genomics