Tools   Select Another Resource Report Type

http://resexomedb.bioinf-dz.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. An online catalog for whole-exome sequencing (WES) results including mutations and gene-disease associations identified by WES. It is browsable and searchable by mutation, gene, study or publication. In addition, it centralizes all publications, software, platforms related to exome / whole genome sequencing.

Proper citation: resExomeDB (RRID:SCR_003224) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/xorro-overlap/

Efficient paired-read overlap software program for use with Illumina sequencing.

Proper citation: XORRO (RRID:SCR_003181) Copy   

•   Source: SciCrunch Registry

http://www.gimp.org

A software application for such tasks as photo retouching, image composition and image authoring. It has many capabilities such as it can be used as a simple paint program, an expert quality photo retouching program, an online batch processing system, a mass production image renderer, an image format converter, etc. GIMP is expandable and extensible and designed to be augmented with plug-ins and extensions. The advanced scripting interface allows everything from the simplest task to the most complex image manipulation procedures to be easily scripted.

Proper citation: GNU Image Manipulation Program (RRID:SCR_003182) Copy   

•   Source: SciCrunch Registry

https://rostlab.org/owiki/index.php/PredictNLS

Software automated tool for analysis and determination of Nuclear Localization Signals (NLS). Predicts that your protein is nuclear or finds out whether your potential NLS is found in our database. The program also compiles statistics on the number of nuclear/non-nuclear proteins in which your potential NLS is found. Finally, proteins with similar NLS motifs are reported, and the experimental paper describing the particular NLS are given.

Proper citation: PredictNLS (RRID:SCR_003133) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/APO

A structured controlled vocabulary for the phenotypes of Ascomycete fungi.

Proper citation: Ascomycete Phenotype Ontology (RRID:SCR_003254) Copy   

•   Source: SciCrunch Registry

http://www.crdamc.amedd.army.mil/behav-health/strong-star.aspx

A multidisciplinary and multi-institutional research consortium to develop and evaluate the most effective early interventions possible for the detection, prevention, and treatment of combatrelated posttraumatic stress disorder (PTSD) in activeduty military personnel and recently discharged veterans. Complementary investigations are focused on the root causes of PTSD, including biological factors that influence PTSD susceptibility and recovery; the influence of comorbid physical and psychological ailments; and the interaction of cognitive-behavioral therapies and pharmacologic treatments. The full cohort of STRONG STAR trials include: Treatment Studies, Biological Studies, Epidemiological Studies, and Preclinical Studies. STRONG STAR is currently conducting three clinical treatment trials at Carl R. Darnall Army Medical Center (CRDAMC). The studies are examining the effectiveness of Cognitive Processing Therapy (CPT), Prolonged Exposure Therapy (PE) and Cognitive Behavioral Therapy for Insomnia (CBTi) with active duty service members. Treatments are offered in individual, group, and online formats, and last from two to eight weeks. Study participants must be active duty service members who will remain in the Ft Hood area for at least 34 months to complete initial assessments and treatment programs. Referrals to the treatment studies can be made through a behavioral health provider or through selfreferral., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Strong Star (RRID:SCR_003132) Copy   

•   Source: SciCrunch Registry

https://github.com/arq5x/lumpy-sv/

Software package as probabilistic framework for structural variant discovery. Capable of integrating any number of SV detection signals including those generated from read alignments or prior evidence. Simplified wrapper for standard analyses, LUMPY Express, can also be executed.

Proper citation: LUMPY (RRID:SCR_003253) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/bcgo-ontology/

An application ontology built for the Beta Cell Genomics database aiming to support database annotation, complicated semantic queries, and automated cell type classification. The ontology is developed using Basic Formal Ontology (BFO) as upper ontology, Ontology for Biomedical Investigations (OBI) as ontology framework and integrated subsets of multiple OBO Foundry (candidate) ontologies. Current the BCGO contains 2383 classes including terms referencing to 24 various OBO Foundry ontologies including CL, CLO, UBERON, GO, PRO, UO, etc.

Proper citation: Beta Cell Genomics Ontology (RRID:SCR_003259) Copy   

•   Source: SciCrunch Registry

http://compbio.cs.sfu.ca/software-novelseq

Software pipeline to detect novel sequence insertions using high throughput paired-end whole genome sequencing data.

Proper citation: NovelSeq (RRID:SCR_003136) Copy   

•   Source: SciCrunch Registry

http://mrcanavar.sourceforge.net/

Copy number caller that analyzes the whole-genome next-generation sequence mapping read depth to discover large segmental duplications and deletions. It also has the capability of predicting absolute copy numbers of genomic intervals.

Proper citation: mrCaNaVaR (RRID:SCR_003135) Copy   

•   Source: SciCrunch Registry

http://www.ichip.de/software/SplicingCompass.html

Software for detection of differential splicing between two different conditions using RNA-Seq data.

Proper citation: SplicingCompass (RRID:SCR_003249) Copy   

•   Source: SciCrunch Registry

http://www.mugen-noe.org/database/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023. MUGEN Mouse Database (MMdb) is a virtual and fully searchable repository of murine models of immune processes and immunological diseases. MMdb is being developed within the context of the MUGEN network of Excellence, a consortium of 21 leading research institutes and universities, and currently holds all mutant mouse models that were developed within the consortium. Its primary aim is to enable information exchange between participating institutions on mouse strain characteristics and availability. More importantly, it aims to create a mouse-centric international forum on modelling of immunological diseases and pave the way to systems biology of the mouse by correlating various genotypic and phenotypic characteristics. The basic categorization of models is based on three major research application categories: * Model of Human Disease * Model of Immune Processes * Transgenic Tool Mutant strains carry detailed information on affected gene(s), mutant alleles and genetic background (DNA origin, targeted, host and backcrossing background). Each gene/transgene index also includes IDs and direct links to Ensembl (EBI��s genome browser), ArrayExpress (providing expression profiles), Eurexpress II (for embryonic expression patterns) and NCBI��s Entrez Gene database. Phenotypic description is standardized and hierarchically structured, based on MGI��s mammalian phenotypic ontology terms, but also includes relevant images and references. Since version 2.1.0 MMdb is also utilizing PATO. Availability (in the form of live mice, cryopreserved embryos or sperm, as well as ES cells) is clearly indicated, along with handling and genotyping details (in the form of documents or hyperlinks) and all relevant contact information (including EMMA and JAX hyperlinks where available).

Proper citation: MUGEN Mouse Database (RRID:SCR_003243) Copy   

•   Source: SciCrunch Registry

http://childes.talkbank.org/

Child language component of TalkBank system. TalkBank is system for sharing and studying conversational interactions. Includes software developed for speech recognition and analysis as well as behavior recognition. Database contains transcript and media data collected from conversations between young children and their playmates and caretakers. Conversations with older children and adults are available from TalkBank. All of data is transcribed in CHAT and CA/CHAT formats.

Proper citation: Child Language Data Exchange System (CHILDES) (RRID:SCR_003241) Copy   

•   Source: SciCrunch Registry

http://www.pathguide.org/

Catalog containing information about 547 biological pathway related resources and molecular interaction related resources. Databases that are free and those supporting BioPAX, CellML, PSI-MI or SBML standards are respectively indicated.

Proper citation: PathGuide: the pathway resource list (RRID:SCR_003248) Copy   

•   Source: SciCrunch Registry

http://www.arnoldfoundation.org/

Private foundation whose funding activities are primarily centered around improving life in the United States. Its mission is to produce big and lasting changes in society over the long term. Their four areas of focus (2014) are: criminal justice, K-12 education, public accountability, and research integrity.

Proper citation: Laura and John Arnold Foundation (RRID:SCR_003240) Copy   

•   Source: SciCrunch Registry

https://osf.io/

Platform to support research and enable collaboration. Used to discover projects, data, materials, and collaborators helpful to your own research.

Proper citation: Open Science Framework (RRID:SCR_003238) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/primerdesigner/

High throughput PCR primer design software. Target regions defined through a rich set of descriptors, such as Ensembl accessions and arbitrary genomic coordinates, may be specified. Primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the specified target regions. As part of the tiling process, primer pairs are computationally screened to meet the criteria for success with one of two PCR amplification protocols.

Proper citation: JCVI Primer Designer (RRID:SCR_003275) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/saskprimerfs/

Software pipeline for designing gene family specific PCR primers. It infers intronic regions of a target species and design for them by utilizing DNA sequence information from a reference organism.

Proper citation: SaskPrimerFS (RRID:SCR_003159) Copy   

•   Source: SciCrunch Registry

http://rostlab.org/services/nlsdb/

A database of nuclear localization signals (NLSs) and of nuclear proteins targeted to the nucleus by NLS motifs. NLSs are short stretches of residues mediating transport of nuclear proteins into the nucleus. The database contains 114 experimentally determined NLSs that were obtained through an extensive literature search. Using "in silico mutagenesis" this set was extended to 308 experimental and potential NLSs. This final set matched over 43% of all known nuclear proteins and matches no currently known non-nuclear protein. NLSdb contains over 6000 predicted nuclear proteins and their targeting signals from the PDB and SWISS-PROT/TrEMBL databases. The database also contains over 12 500 predicted nuclear proteins from six entirely sequenced eukaryotic proteomes (Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana and Saccharomyces cerevisiae). NLS motifs often co-localize with DNA-binding regions. This observation was used to also annotate over 1500 DNA-binding proteins. From this site you can: * Query NLSdb * Find out how to use NLSdb * Browse the entries in NLSdb * Find out if your protein has an NLS using PredictNLS * Predict subcellular localization of your protein using LOCtree

Proper citation: NLSdb: a database of nuclear localization signals (RRID:SCR_003273) Copy   

•   Source: SciCrunch Registry

http://abi.inf.uni-tuebingen.de/Services/MultiLoc2

An extensive high-performance subcellular protein localization prediction system that incorporates phylogenetic profiles and Gene Ontology terms to yield higher accuracies compared to its previous version. Moreover, it outperforms other prediction systems in two benchmarks studies. A downloadable version of MultiLoc2 for local use is also available.

Proper citation: MultiLoc (RRID:SCR_003151) Copy   

•   Source: SciCrunch Registry