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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
BaCelLo Resource Report Resource Website 10+ mentions |
BaCelLo (RRID:SCR_011965) | BaCelLo | data analysis service, production service resource, service resource, analysis service resource | A predictor for the subcellular localization of proteins in eukaryotes that is based on a decision tree of several support vector machines (SVMs). It classifies up to four localizations for Fungi and Metazoan proteins and five localizations for Plant ones. BaCelLo's predictions are balanced among different classes and all the localizations are considered as equiprobable. | protein, data set, proteome |
is listed by: OMICtools is listed by: SoftCite has parent organization: University of Bologna; Bologna; Italy |
PMID:16873501 | OMICS_01616 | SCR_011965 | 2026-02-13 10:56:50 | 45 | ||||||||
|
Smart Dictionary Lookup Resource Report Resource Website |
Smart Dictionary Lookup (RRID:SCR_000568) | Smart Dictionary Lookup | data or information resource, service resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 9, 2022. System that retrieves relevant UniProt IDs from BioThesaurus entries using a soft string matching algorithm. | gene, protein |
uses: UniProt uses: BioThesaurus is listed by: OMICtools has parent organization: University of Manchester; Manchester; United Kingdom |
PMID:17698493 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01198 | SCR_000568 | 2026-02-13 10:54:42 | 0 | |||||||
|
MAPPER - Multi-genome Analysis of Positions and Patterns of Elements of Regulation Resource Report Resource Website 10+ mentions |
MAPPER - Multi-genome Analysis of Positions and Patterns of Elements of Regulation (RRID:SCR_003077) | MAPPER, MAPPER 2, | data or information resource, service resource, database | A platform composed of three modules: the Database, the Search Engine, and rSNPs, for the computational identification of transcription factor binding sites (TFBSs) in multiple genomes, that combines TRANSFAC and JASPAR data with the search power of profile hidden Markov models (HMMs). The Database contains putative TFBSs found in the upstream sequences of genes from the human, mouse and D.melanogaster genomes. For each gene, they scanned the region from 10,000 base pairs upstream of the transcript start to 50 base pairs downstream of the coding sequence start against all their models. Therefore, the database contains putative binding sites in the gene promoter and in the initial introns and non-coding exons. Information displayed for each putative binding site includes the transcription factor name, its position (absolute on the chromosome, or relative to the gene), the score of the prediction, and the region of the gene the site belongs to. If the selected gene has homologs in any of the other two organisms, the program optionally displays the putative TFBSs in the homologs. The Search Engine allows the identification, visualization and selection of putative TFBSs occurring in the promoter or other regions of a gene from the human, mouse, D.melanogaster, C.elegans or S.cerevisiae genomes. In addition, it allows the user to upload a sequence to query and to build a model by supplying a multiple sequence alignment of binding sites for a transcription factor of interest. rSNPs MAPPER is designed to identify Single Nucleotide Polymorphisms (SNPs) that may have an effect on the presence of one or more TFBSs. | transcription factor binding site, gene promoter, intron, non-coding exon, transcription factor, chromosome, gene, homolog, rsnp, single nucleotide polymorphism, search engine |
is listed by: OMICtools has parent organization: University of Florida; Florida; USA is parent organization of: rSNPs MAPPER |
PMID:15608292 PMID:15799782 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01877, nif-0000-03101 | http://bio.chip.org/mapper | SCR_003077 | Multi-genome Analysis of Positions and Patterns of Elements of Regulation, MAPPER 2 - Multi-genome Analysis of Positions and Patterns of Elements of Regulation, MAPPER database | 2026-02-13 10:55:10 | 11 | |||||
|
HomoloGene Resource Report Resource Website 100+ mentions |
HomoloGene (RRID:SCR_002924) | HomoloGene | data or information resource, service resource, database | Automated system for constructing putative homology groups from complete gene sets of wide range of eukaryotic species. Databse that provides system for automatic detection of homologs, including paralogs and orthologs, among annotated genes of sequenced eukaryotic genomes. HomoloGene processing uses proteins from input organisms to compare and sequence homologs, mapping back to corresponding DNA sequences. Reports include homology and phenotype information drawn from Online Mendelian Inheritance in Man, Mouse Genome Informatics, Zebrafish Information Network, Saccharomyces Genome Database and FlyBase. | homolog, paralog, ortholog, genome, gene, protein, protein alignment, phenotype, conserved domain, homology, amino acid sequence, cell, dna, gold standard |
is used by: NIF Data Federation is used by: Nowomics is used by: MitoMiner is listed by: OMICtools is listed by: re3data.org is related to: OMIM is related to: Mouse Genome Informatics (MGI) is related to: Zebrafish Information Network (ZFIN) is related to: SGD is related to: FlyBase is related to: ProbeMatchDB 2.0 is related to: Biomine is related to: Consensus CDS has parent organization: NCBI |
PMID:23193264 | Free, Freely availalbe | nif-0000-02975, r3d100010781, OMICS_01544 | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene https://doi.org/10.17616/R3889F |
SCR_002924 | NCBI HomoloGene | 2026-02-13 10:55:08 | 437 | |||||
|
ResponseNet Resource Report Resource Website 1+ mentions |
ResponseNet (RRID:SCR_003176) | ResponseNet | data analysis service, production service resource, service resource, analysis service resource | WebServer that identifies high-probability signaling and regulatory paths that connect input data sets. The input includes two weighted lists of condition-related proteins and genes, such as a set of disease-associated proteins and a set of differentially expressed disease genes, and a molecular interaction network (i.e., interactome). The output is a sparse, high-probability interactome sub-network connecting the two sets that is biased toward signaling pathways. This sub-network exposes additional proteins that are potentially involved in the studied condition and their likely modes of action. Computationally, it is formulated as a minimum-cost flow optimization problem that is solved using linear programming. | interactome, gene, protein, signaling pathway, signaling, regulatory, pathway, regulatory pathway, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Ben-Gurion University of the Negev; Beer-Sheva; Israel |
PMID:23761447 PMID:21576238 |
Free, Freely available | biotools:responsenet, OMICS_01562 | https://bio.tools/responsenet | http://netbio.bgu.ac.il/respnet/ | SCR_003176 | 2026-02-13 10:55:11 | 4 |
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