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http://ccb.jhu.edu/software/tophat/index.shtml

Software tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions.

Proper citation: TopHat (RRID:SCR_013035) Copy   

•   Source: SciCrunch Registry

http://mitobreak.portugene.com/cgi-bin/Mitobreak_home.cgi

Database with curated datasets of mitochondrial DNA (mtDNA) rearrangements. Users may submit new mtDNA rearrangements.

Proper citation: MitoBreak (RRID:SCR_012949) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/minfi.html

Software tools for analyzing and visualizing Illumina''s 450k array data.

Proper citation: minfi (RRID:SCR_012830) Copy   

•   Source: SciCrunch Registry

http://www.imgt.org/

A high-quality integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrate species, and in the immunoglobulin superfamily (IgSF), MHC superfamily (MhcSF) and related proteins of the immune system (RPI) of vertebrates and invertebrates, serving as the global reference in immunogenetics and immunoinformatics. IMGT provides a common access to sequence, genome and structure Immunogenetics data, based on the concepts of IMGT-ONTOLOGY and on the IMGT Scientific chart rules. IMGT works in close collaboration with EBI (Europe), DDBJ (Japan) and NCBI (USA). IMGT consists of sequence databases, genome database, structure database, and monoclonal antibodies database, Web resources and interactive tools.

Proper citation: IMGT - the international ImMunoGeneTics information system (RRID:SCR_012780) Copy   

•   Source: SciCrunch Registry

http://ekhidna.biocenter.helsinki.fi/dali_server

Network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank (PDB). You receive an email notification when the search has finished. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences. Requests can also be submitted by e-mail to dali-server at helsinki dot fi. The body of the e-mail message must contain atomic coordinates in PDB format. If you want to know the structural neighbours of a protein already in the Protein Data Bank (PDB), you can find them in the Dali Database. If you want to superimpose two particular structures, you can do it in the pairwise DaliLite server. Academic users may download the DaliLite program for local use.

Proper citation: Dali Server (RRID:SCR_013433) Copy   

•   Source: SciCrunch Registry

http://shelx.uni-ac.gwdg.de/SHELX/

A set of software programs that utilizes dual spaces algorithms for the determination of small and macromolecular crystal structures by single crystal X-ray and neutron diffraction. Libraries, extra files and environment variables are not required for the executables. SHELX is intended to be run on a command prompt but may be called from GUIs such as shelXle, Olex2, Oscail or WinGX, or hkl2map., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SHELX (RRID:SCR_014220) Copy   

•   Source: SciCrunch Registry

http://www.psygenet.org/web/PsyGeNET/menu;jsessionid=y6kqy9lqlxymr0nwwkkfo84

Knowledge platform on psychiatric disorders and their genes. Resource for exploratory analysis of psychiatric diseases and their associated genes. PsyGeNET is composed of database and set of analysis tools and is the result of the integration of information from DisGeNET and data extracted from the literature by text mining, followed by curation by domain experts.

Proper citation: PsyGeNET (RRID:SCR_014406) Copy   

•   Source: SciCrunch Registry

http://copasi.org/

Software application for simulation and analysis of biochemical network models and their dynamics. COPASI supports models in the SBML standard and can simulate their behavior using ODEs or Gillespies stochastic simulation algorithm. Arbitrary discrete events can be included in such simulations. Models in COPASI are based on reactions that convert a set of species into another set of species. Simulation can be performed either with stochastic kinetics or with differential equations. COPASI also includes various methods of analysis and data visualization.

Proper citation: COPASI (RRID:SCR_014260) Copy   

•   Source: SciCrunch Registry

http://scratch.proteomics.ics.uci.edu/index.html

Web protein structure and structural feature prediction server.Software suite includes predictors for secondary structure, relative solvent accessibility, disordered regions, domains, disulfide bridges, single mutation stability, residue contacts versus average, individual residue contacts and tertiary structure. User provides amino acid sequence and selects desired predictions, then submits to the server.

Proper citation: SCRATCH (RRID:SCR_014291) Copy   

•   Source: SciCrunch Registry

http://sysbio.rnet.missouri.edu/multicom_toolbox/NNCon%201.0.html

Protein contact map prediction is useful for protein folding rate prediction, model selection and 3D structure prediction. Here we describe NNcon, a fast and reliable contact map prediction server and software. NNcon was ranked among the most accurate residue contact predictors in the Eighth Critical Assessment of Techniques for Protein Structure Prediction (CASP8), 2008.

Proper citation: NNcon (RRID:SCR_014292) Copy   

•   Source: SciCrunch Registry

http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/

Software for macromolecular model building, model completion and validation, and protein modelling using X-ray data. Coot displays maps and models and allows model manipulations such as idealization, rigid-body fitting, ligand search, Ramachandran plots, non-crystallographic symmetry and more. Source code is available.

Proper citation: Coot (RRID:SCR_014222) Copy   

•   Source: SciCrunch Registry

http://cns-online.org/v1.2/

Software designed to provide a multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination. Features include heavy atom searching, experimental phasing (including MAD and MIR), density modification, crystallographic refinement with maximum likelihood targets, and NMR structure calculation using NOEs, J-coupling, chemical shift, and dipolar coupling data. Modules, libraries, utility programs, tutorials, and a syntax manual are available on the website.

Proper citation: Crystallography and NMR System (CNS) (RRID:SCR_014223) Copy   

•   Source: SciCrunch Registry

http://bix.ucsd.edu/repeatscout/

Algorithm used to identify de novo repeat families in newly sequenced genomes. Repeat libraries for C. briggsae, M. muscles (X chromosome), R. novegicus (X chromosome), armadillo, H. sapiens (X chromosome), and various other mammals created using RepeatScout are available on the main site., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: RepeatScout (RRID:SCR_014653) Copy   

•   Source: SciCrunch Registry

http://cole-trapnell-lab.github.io/cufflinks/cuffmerge/

Software tool for transcriptome assembly and differential expression analysis for RNA-Seq. Includes script called cuffmerge that can be used to merge together several Cufflinks assemblies. It also handles running Cuffcompare as well as automatically filtering a number of transfrags that are likely to be artifacts. If the researcher has a reference GTF file, the researcher can provide it to the script to more effectively merge novel isoforms and maximize overall assembly quality.

Proper citation: Cufflinks (RRID:SCR_014597) Copy   

•   Source: SciCrunch Registry

http://rast.nmpdr.org

A SEED-quality automated service that annotates complete or nearly complete bacterial and archaeal genomes across the entire phylogenetic tree. RAST can also be used to analyze draft genomes.

Proper citation: RAST Server (RRID:SCR_014606) Copy   

•   Source: SciCrunch Registry

http://www.vicbioinformatics.com/software.prokka.shtml

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for the rapid annotation of prokaryotic genomes. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Prokka (RRID:SCR_014732) Copy   

•   Source: SciCrunch Registry

http://www.sailing.cs.cmu.edu/main/?page_id=511

Automatic software program for profiling spatial gene expression patterns from Fly embryo ISH images. It utilizes image-based genome-scale profiling of whole-body mRNA patterns.

Proper citation: SPEX2 (RRID:SCR_014923) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.psb.ugent.be/orcae/

Online genome annotation tool for validating and correcting gene annotations. OrcAE is community-driven and can be edited by account-holders in the research community.

Proper citation: Online Resource for Community Annotation of Eukaryotes (RRID:SCR_014989) Copy   

•   Source: SciCrunch Registry

http://www.mybiosoftware.com/seaview-4-2-12-sequence-alignment-phylogenetic-tree-building.html

Graphical user interface for multiple sequence alignment and molecular phylogeny. SeaView also generates phylogenetic trees.

Proper citation: SeaView (RRID:SCR_015059) Copy   

•   Source: SciCrunch Registry

http://www.stavroX.com

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 29,2023. Software tool for the analysis of cross-linking/mass spectrometry datasets using MS-cleavable cross-linkers. MeroX is specialized for MS/MS-cleavable cross linking reagents and identifies the specific fragmentation products of the cleavable cross links.

Proper citation: MeroX (RRID:SCR_014956) Copy   

•   Source: SciCrunch Registry