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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
Service that partners with independent scholarly publishers, societies, associations, and university presses to facilitate the digital dissemination of 1779 journals, reference works, books, and proceedings. It also offers a complete manuscript submission, tracking, peer review, and publishing system for journal editors.
Proper citation: HighWire (RRID:SCR_005316) Copy
https://sites.google.com/site/jpopgen/dbNSFP
A database for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome. Version 2.0 is based on the Gencode release 9 / Ensembl version 64 and includes a total of 87,347,043 nsSNVs and 2,270,742 essential splice site SNVs. It compiles prediction scores from six prediction algorithms (SIFT, Polyphen2, LRT, MutationTaster, MutationAssessor and FATHMM), three conservation scores (PhyloP, GERP++ and SiPhy) and other related information including allele frequencies observed in the 1000 Genomes Project phase 1 data and the NHLBI Exome Sequencing Project, various gene IDs from different databases, functional descriptions of genes, gene expression and gene interaction information, etc. Some dbNSFP contents (may not be up-to-date though) can also be accessed through variant tools, ANNOVAR, KGGSeq, UCSC Genome Browser''s Variant Annotation Integrator, Ensembl Variant Effect Predictor and HGMD.
Proper citation: dbNSFP (RRID:SCR_005178) Copy
http://swissregulon.unibas.ch/fcgi/sr/swissregulon
A database of genome-wide annotations of regulatory sites. The predictions are based on Bayesian probabilistic analysis of a combination of input information including: * Experimentally determined binding sites reported in the literature. * Known sequence-specificities of transcription factors. * ChIP-chip and ChIP-seq data. * Alignments of orthologous non-coding regions. Predictions were made using the PhyloGibbs, MotEvo, IRUS and ISMARA algorithms developed in their group, depending on the data available for each organism. Annotations can be viewed in a Gbrowse genome browser and can also be downloaded in flat file format.
Proper citation: SwissRegulon (RRID:SCR_005333) Copy
http://www2.hu-berlin.de/wikizbnutztier/software/CandiSNPer/
A webtool which helps in characterizing Single Nucleotide Polymorphisms (SNPs) that are located in the vicinity of an SNP of interest (start SNP). Along with the computation of the maximal Linkage Disequilibrium (LD) region around the start SNP. CandiSNPer provides additional information with respect to the molecular consequences of the SNPs and the genes located in the LD region.
Proper citation: CandiSNPer (RRID:SCR_005173) Copy
http://wishart.biology.ualberta.ca/polysearch/index.htm
A web-based tool that supports more than 50 different classes of queries against nearly a dozen different types of text, scientific abstract or bioinformatic databases. The typical query supported by PolySearch is Given X, find all Y''s where X or Y can be diseases, tissues, cell compartments, gene/protein names, SNPs, mutations, drugs and metabolites. PolySearch also exploits a variety of techniques in text mining and information retrieval to identify, highlight and rank informative abstracts, paragraphs or sentences.
Proper citation: PolySearch (RRID:SCR_005291) Copy
http://katahdin.mssm.edu/kismeth/revpage.pl
A web-based tool for bisulfite sequencing analysis that was designed to be used with plants, since it considers potential cytosine methylation in any sequence context (CG, CHG, and CHH). It provides a tool for the design of bisulfite primers as well as several tools for the analysis of the bisulfite sequencing results. Kismeth is not limited to data from plants, as it can be used with data from any species.
Proper citation: Kismeth (RRID:SCR_005444) Copy
http://fairbrother.biomed.brown.edu/spliceman/index.cgi
An online tool that takes a set of DNA sequences with point mutations and returns a ranked list to predict the effects of point mutations on pre-mRNA splicing. The current implementation includes 11 genomes: human, chimp, rhesus, mouse, rat, dog, cat, chicken, guinea pig, frog and zebrafish.
Proper citation: Spliceman (RRID:SCR_005354) Copy
http://the_brain.bwh.harvard.edu/uniprobe/
Database that hosts experimental data from universal protein binding microarray (PBM) experiments (Berger et al., 2006) and their accompanying statistical analyses from prokaryotic and eukaryotic organisms, malarial parasites, yeast, worms, mouse, and human. It provides a centralized resource for accessing comprehensive data on the preferences of proteins for all possible sequence variants ("words") of length k ("k-mers"), as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data. The database's web tools include a text-based search, a function for assessing motif similarity between user-entered data and database PWMs, and a function for locating putative binding sites along user-entered nucleotide sequences.
Proper citation: UniPROBE (RRID:SCR_005803) Copy
A web server that predicts the functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or nonsynonymous polymorphisms. The functional impact is assessed based on evolutionary conservation of the affected amino acid in protein homologs. The method has been validated on a large set (51k) of disease associated (OMIM) and polymorphic variants., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MutationAssessor (RRID:SCR_005762) Copy
http://gopubmed.org/web/gopubmed/
A web server which allows users to explore PubMed search results with the Gene Ontology, a hierarchically structured vocabulary for molecular biology. GoPubMed submits a user''''s keywords to PubMed, retrieves the abstracts, detects Gene Ontology terms in the abstracts, displays the subset of Gene Ontology relevant to the original query, and allows the user to browse through the ontology displaying associated papers and their GO annotation. Platform: Online tool
Proper citation: GoPubMed (RRID:SCR_005823) Copy
http://agbase.msstate.edu/cgi-bin/tools/goslimviewer_select.pl
Service to summarize the GO function associated with a data set using prepared GO Slim sets. The input is a tab separated list of gene product IDs and GO IDs.
Proper citation: GOSlimViewer (RRID:SCR_005665) Copy
A Galaxy framework-based online pipeline for reliable analysis of data generated by three types of CLIP-seq protocols: HITS-CLIP, PAR-CLIP and iCLIP. It provides both data processing and statistical analysis to determine candidate cross-linking regions, which are comparable to those regions identified from the original studies or using existing computational tools., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: PIPE-CLIP (RRID:SCR_005820) Copy
A next-generation web-based application that aims to provide an integrated solution for both visualization and analysis of deep-sequencing data, along with simple access to public datasets.
Proper citation: Systems Transcriptional Activity Reconstruction (RRID:SCR_005622) Copy
http://mint.bio.uniroma2.it/virusmint/
A virus protein interactions database that collects and annotates all the interactions between human and viral proteins and integrates this information in the human protein interaction network. It uses the PSI-MI standard and is fully integrated with the MINT database. You can search for any viral or human protein by entering either common names or database identifiers or display a complete viral interactome.
Proper citation: VirusMINT (RRID:SCR_005987) Copy
http://www.gene-regulation.com/pub/databases.html#transfac
Manually curated database of eukaryotic transcription factors, their genomic binding sites and DNA binding profiles. Used to predict potential transcription factor binding sites.
Proper citation: TRANSFAC (RRID:SCR_005620) Copy
http://www.informatics.jax.org
International database for laboratory mouse. Data offered by The Jackson Laboratory includes information on integrated genetic, genomic, and biological data. MGI creates and maintains integrated representation of mouse genetic, genomic, expression, and phenotype data and develops reference data set and consensus data views, synthesizes comparative genomic data between mouse and other mammals, maintains set of links and collaborations with other bioinformatics resources, develops and supports analysis and data submission tools, and provides technical support for database users. Projects contributing to this resource are: Mouse Genome Database (MGD) Project, Gene Expression Database (GXD) Project, Mouse Tumor Biology (MTB) Database Project, Gene Ontology (GO) Project at MGI, and MouseCyc Project at MGI.
Proper citation: Mouse Genome Informatics (MGI) (RRID:SCR_006460) Copy
http://panoga.sabanciuniv.edu/
A web server to devise functionally important pathways through the identification of single nucleotide polymorphism (SNP)-targeted genes within these pathways. The strength of the methodology stems from its multidimensional perspective, where evidence from the following five resources is combined: (i) genetic association information obtained through GWAS, (ii) SNP functional information, (iii) protein-protein interaction network, (iv) linkage disequilibrium and (v) biochemical pathways.
Proper citation: PANOGA (RRID:SCR_006242) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. Software application for pedigree drawing (entry from Genetic Analysis Software)
Proper citation: Pedigree-Draw (RRID:SCR_008302) Copy
European website providing information about orphan drugs and rare diseases. It contains content both for physicians and for patients. Reference portal for rare diseases and orphan drugs to help improve diagnosis, care and treatment of patients with rare diseases.
Proper citation: Orphanet (RRID:SCR_006628) Copy
https://chlorobox.mpimp-golm.mpg.de/geseq.html
Software tool for rapid and accurate annotation of organelle genomes, in particular chloroplast genomes.
Proper citation: GeSeq (RRID:SCR_017336) Copy
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