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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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University of California at Los Angeles - Department of Energy Institute for Genomics and Proteomics Resource Report Resource Website 1+ mentions |
University of California at Los Angeles - Department of Energy Institute for Genomics and Proteomics (RRID:SCR_001921) | data computation service, organization portal, database, portal, data or information resource | The UCLA-DOE Institute for Genomics and Proteomics carries out research in bioenergy, structural biology, genomics and proteomics, consistent with the research mission of the United States Department of Energy. Major interests of the 12 Principal Investigators and 9 Associate Members include systems approaches to organisms, structural biology, bioinformatics, and bioenergetic systems. The Institute sponsors 5 Core Technology Centers, for X-ray and NMR structural determination, bioinformatics and computation, protein expression and purification, and biochemical instrumentation. Services offered by this Institute: - Databases: * DIP (The Database of Interacting Proteins): The DIPTM database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. * ProLinks Database of Functional Linkages: The Prolinks database is a collection of inference methods used to predict functional linkages between proteins. These methods include the Phylogenetic Profile method which uses the presence and absence of proteins across multiple genomes to detect functional linkages; the Gene Cluster method, which uses genome proximity to predict functional linkage; Rosetta Stone, which uses a gene fusion event in a second organism to infer functional relatedness; and the Gene Neighbor method, which uses both gene proximity and phylogenetic distribution to infer linkage. - Data-to-Structure Servers: * SAVEs Structure Verification Server * Merohedral Twinning Test Server * SER Surface Entropy Reduction Server * VERIFY3D Structure Verification Server * ERRAT Structure Verification Server - Structure-to-Function Servers: * ProKnow Protein Functionator * Hot Patch Functional Site Locator | expression, functional linkage, gene, biochemical instrumentation, bioenergetic system, bioenergy, bioinformatic, computation, genome, genomic, nmr, organism, protein, protein-protein interaction, proteomic, purification, structural biology, x-ray | nif-0000-10491 | SCR_001921 | UCLA-DOE | 2026-02-16 09:45:40 | 4 | ||||||||||
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Stanford Genomic Resourses Resource Report Resource Website |
Stanford Genomic Resourses (RRID:SCR_001874) | data or information resource, topical portal, portal | This resource hyperlinks to systematic analysis projects, resources, laboratories, and departments at Stanford University. | gene, genes, aspergillus, candida, genome, genomics, human, mouse | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10436 | SCR_001874 | Genomic Databases | 2026-02-16 09:45:36 | 0 | |||||||||
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MEME Suite - Motif-based sequence analysis tools Resource Report Resource Website 1000+ mentions |
MEME Suite - Motif-based sequence analysis tools (RRID:SCR_001783) | MEME Suite | software application, data processing software, data analysis software, data analysis service, analysis service resource, software resource, database, source code, production service resource, service resource, data or information resource | Suite of motif-based sequence analysis tools to discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences; search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN; compare a motif to all motifs in a database of motifs; associate motifs with Gene Ontology terms via their putative target genes, and analyze motif enrichment using SpaMo or CentriMo. Source code, binaries and a web server are freely available for noncommercial use. | gene ontology, motif, comparative genomics, dna regulatory motif, dna sequence, dna, gene, transcription factor, genome, protein, analysis, function analysis, comparison, cluster, enrichment analysis, sequence analysis, bio.tools, FASEB list |
lists: DREME is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Glam2 is related to: ANNOgesic is related to: memesuite-lite has parent organization: National Biomedical Computation Resource is parent organization of: GOMO - Gene Ontology for Motifs |
NCRR R01 RR021692 | PMID:19458158 DOI:10.1093/nar/gkl198 |
Free, Freely available | nif-0000-10298, biotools:meme_suite, OMICS_08103 | https://bio.tools/meme_suite | http://meme.sdsc.edu/meme4_6_1/intro.html, http://meme.nbcr.net/meme/, https://sources.debian.org/src/meme/ | SCR_001783 | The MEME Suite | 2026-02-16 09:45:37 | 2091 | |||
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AStalavista Resource Report Resource Website 50+ mentions |
AStalavista (RRID:SCR_001815) | AStalavista | data analysis service, analysis service resource, software resource, production service resource, service resource | Tool that extracts and displays alternative splicing (AS) events from a given genomic annotation of exon-intron gene coordinates. By comparing all given transcripts, it detects the variations in their splicing structure and identifies all AS events (like exon skipping, alternate donor, etc) by assigning to each of them an AS code. It provides a visual summary of the AS landscape in the analyzed dataset, the possibility to browse the results on the UCSC website or to download them in GTF or ASTA format. You can use AStalavista for any genome by providing your own annotation set, the identifier of your gene(s) of interest, or analyze the AS landscape of reference annotation datasets like Gencode, RefSeq, Ensembl, FlyBase, etc. | alternative splicing event, alternative splicing, visualization, genome, transcript |
is listed by: OMICtools is listed by: SoftCite has parent organization: Center for Genomic Regulation; Barcelona; Spain |
PMID:17485470 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01943 | http://genome.imim.es/astalavista http://genome.crg.es/astalavista/ |
SCR_001815 | Alternative Splicing transcriptional landscape visualization tool | 2026-02-16 09:45:36 | 83 | |||||
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LegumeIP Resource Report Resource Website 10+ mentions |
LegumeIP (RRID:SCR_008906) | LegumeIP | data analysis service, analysis service resource, database, production service resource, service resource, data or information resource | LegumeIP is an integrative database and bioinformatics platform for comparative genomics and transcriptomics to facilitate the study of gene function and genome evolution in legumes, and ultimately to generate molecular based breeding tools to improve quality of crop legumes. LegumeIP currently hosts large-scale genomics and transcriptomics data, including: * Genomic sequences of three model legumes, i.e. Medicago truncatula, Glycine max (soybean) and Lotus japonicus, including two reference plant species, Arabidopsis thaliana and Poplar trichocarpa, with the annotation based on UniProt TrEMBL, InterProScan, Gene Ontology and KEGG databases. LegumeIP covers a total 222,217 protein-coding gene sequences. * Large-scale gene expression data compiled from 104 array hybridizations from L. japonicas, 156 array hybridizations from M. truncatula gene atlas database, and 14 RNA-Seq-based gene expression profiles from G. max on different tissues including four common tissues: Nodule, Flower, Root and Leaf. * Systematic synteny analysis among M. truncatula, G. max, L. japonicus and A. thaliana. * Reconstruction of gene family and gene family-wide phylogenetic analysis across the five hosted species. LegumeIP features comprehensive search and visualization tools to enable the flexible query on gene annotation, gene family, synteny, relative abundance of gene expression. | gene function, genome evolution, legume, gene, genome, plant, genomics, transcriptomic, gene annotation, gene family, synteny, gene expression, blast, genomic sequence, microarray, rna-seq, comparative genomics, bio.tools |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools is related to: UniProt is related to: InterProScan is related to: Gene Ontology is related to: KEGG has parent organization: Samuel Roberts Noble Foundation |
Samuel Roberts Noble Foundation ; NSF ABI-0960897 |
PMID:22110036 | biotools:legumeip, nlx_151455 | https://bio.tools/legumeip | SCR_008906 | LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes, LegumeIP - An Integrative Platform to Study Gene Function and Genome Evolution in Legumes | 2026-02-16 09:47:18 | 19 | |||||
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BeeBase Resource Report Resource Website 50+ mentions |
BeeBase (RRID:SCR_008966) | BeeBase | data set, data analysis service, analysis service resource, database, production service resource, service resource, data or information resource | Gene sequences and genomes of Bombus terrestris, Bombus impatiens, Apis mellifera and three of its pathogens, that are discoverable and analyzed via genome browsers, blast search, and apollo annotation tool. The genomes of two additional species, Apis dorsata and A. florea are currently under analysis and will soon be incorporated.BeeBase is an archive and will not be updated. The most up-to-date bee genome data is now available through the navigation bar on the HGD Home page. | genome, gene set, sequence, bee, genomics, entomology, blast, annotation, pest, pathogen, honey, beehive, insect, bee pollen, bee product, bee culture, pollination, pollinator, bio.tools, FASEB list |
is listed by: re3data.org is listed by: Debian is listed by: bio.tools has parent organization: University of Missouri; Missouri; USA |
Texas Agricultural Experiment Station ; Golden Heritage Foods and Sioux Honey Association ; NHGRI 5-P41-HG000739-13; USDA 2008-35302-18804 |
PMID:21071397 | Open unspecified license, Acknowledgement requested, Data Usage Policy | nlx_152034, biotools:hgd, r3d100010925 | https://bio.tools/hgd https://doi.org/10.17616/R3Z629 |
SCR_008966 | Hymenoptera Genome Database | 2026-02-16 09:47:19 | 56 | ||||
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Renal Disease Portal Resource Report Resource Website |
Renal Disease Portal (RRID:SCR_009030) | Renal Disease Portal | data set, topical portal, portal, data or information resource, disease-related portal | An integrated resource for information on genes, QTLs and strains associated with a variety of kidney and renal system conditions such as Renal Hypertension, Polycystic Kidney Disease and Renal Insufficiency, as well as Kidney Neoplasms. | gene, quantitative trait locus, strain, renal hypertension, kidney neoplasm, phenotype, pathway, biological process, disease, kidney, genome, gviewer, chromosome, molecular function, cellular component, visualization, synteny |
is related to: NIDDK Information Network (dkNET) is related to: Gene Ontology has parent organization: Rat Genome Database (RGD) |
Renal disease, Renal hypertension, Polycystic kidney disease, Renal insufficiency, Kidney neoplasm, Diabetes Insipidus, Hyperoxaluria, Renal hypertension, Nephritis, Nephrocalcinosis, Nephrolithiasis, Nephrosis, Renal Fibrosis, Inborn Error of Renal Tubular Transport, Uremia | nlx_153941 | SCR_009030 | RGD Renal Disease Portal | 2026-02-16 09:47:20 | 0 | |||||||
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SNVrap Resource Report Resource Website 1+ mentions |
SNVrap (RRID:SCR_010512) | web service, data set, data analysis service, analysis service resource, data access protocol, software resource, production service resource, service resource, data or information resource | The web portal provides comprehensive local database of human genome variants with a user-friendly web page that provides a one-stop annotating and funtonal prediction service which is both convenient and up-to-date. A query can be accepted as either a dbSNP Id or a chromosomal location and our system will instantly provide all the annotation information in an interactive LD panel. The system can also simultaneously prioritize this variant based on additive effect mode by corresponding annotation information and evaluate the variant effect that is then displayed in a prioritization tree. Furthermore, cohort sequencing continuously produces lots of un-annotated variants such as rare variants or de novo variants, and our system can even fit this data by accepting genomic coordinates (hg19) to offer maximal annotations. Main Functions Over 40 up-to-date annotation items for human single nucleotide variations; Functional prediction for different types of variants; Dynamic LD panel for both HapMap and 1000 Genomes Project populations; Prioritization score and tree viewer based on variant functional model. | genetic variant, prioritize, genome, chromosome, functional prediction, transcription factor-binding site, mirna, mirna target site, prediction, target site, transcription factor, binding site, statistics, trait/disease-associated snp, single nucleotide polymorphism | PMID:25308971 | nlx_158733 | http://jjwanglab.org/snvrap/snvrap/snvrap/quickrap | SCR_010512 | 2026-02-16 09:47:52 | 4 | |||||||||
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TESS: Transcription Element Search System Resource Report Resource Website 100+ mentions |
TESS: Transcription Element Search System (RRID:SCR_010739) | TESS | data analysis service, analysis service resource, database, production service resource, service resource, data or information resource | TESS is a web tool for predicting transcription factor binding sites in DNA sequences. It can identify binding sites using site or consensus strings and positional weight matrices from the TRANSFAC, JASPAR, IMD, and our CBIL-GibbsMat database. You can use TESS to search a few of your own sequences or for user-defined CRMs genome-wide near genes throughout genomes of interest. Search for CRMs Genome-wide: TESS now has the ability to search whole genomes for user defined CRMs. Try a search in the AnGEL CRM Searches section of the navigation bar.. You can search for combinations of consensus site sequences and/or PWMs from TRANSFAC or JASPAR. Search DNA for Binding Sites: TESS also lets you search through your own sequence for TFBS. You can include your own site or consensus strings and/or weight matrices in the search. Use the Combined Search under ''Site Searches'' in the menu or use the box for a quick search. TESS assigns a TESS job number to all sequence search jobs. The job results are stored on our server for a period of time specified in the search submit form. During this time you may recall the search results using the form on this page. TESS can also email results to you as a tab-delimited file suitable for loading into a spreadsheet program. Query for Transcription Factor Info: TESS also has data browsing and querying capabilities to help you learn about the factors that were predicted to bind to your sequence. Use the Query TRANSFAC or Query Matrices links above or use the search interface provided from the home page. | transcription factor, dna sequence, genome, promoter, gene regulation, FASEB list | has parent organization: University of Pennsylvania; Philadelphia; USA | PMID:18428685 | nlx_97404 | http://www.pcbi.upenn.edu/tess | SCR_010739 | Transcription Element Search System | 2026-02-16 09:47:53 | 189 | ||||||
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BWA Resource Report Resource Website 1000+ mentions |
BWA (RRID:SCR_010910) | BWA | software application, data processing software, sequence analysis software, data analysis software, image analysis software, software resource, alignment software | Software for aligning sequencing reads against large reference genome. Consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. First for sequence reads up to 100bp, and other two for longer sequences ranged from 70bp to 1Mbp. | sequence, alignment, reference, genome, human, short, long, read, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: shovill is related to: Proovread is related to: BWA-MEM2 has parent organization: SourceForge is required by: RelocaTE |
PMID:19451168 PMID:20080505 DOI:10.1093/bioinformatics/btp324 |
Free, Available for download, Freely available | SCR_015853, biotools:bwa-sw, OMICS_00654 | https://sourceforge.net/projects/bio-bwa/files/ https://bio.tools/bwa-sw https://sources.debian.org/src/bwa/ |
SCR_010910 | Burrows-Wheeler Aligner (BWA), Burrows-Wheeler Aligner | 2026-02-16 09:47:54 | 2291 | |||||
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GenomeCloud Resource Report Resource Website |
GenomeCloud (RRID:SCR_011886) | GenomeCloud | service resource, data repository, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 29, 2019. A cloud platform for next-generation sequencing analysis and storage. Services include: * g-Analysis: Automated genome analysis pipelines at your fingertips * g-Cluster: Easy-of-use and cost-effective genome research infrastructure * g-Storage: A simple way to store, share and protect data * g-Insight: Accurate analysis and interpretation of biological meaning of genome data | genome | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01219 | SCR_011886 | 2026-02-16 09:48:04 | 0 | ||||||||
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JiffyNet Resource Report Resource Website 1+ mentions |
JiffyNet (RRID:SCR_011954) | software application, data analysis service, analysis service resource, software resource, simulation software, production service resource, service resource | Web based instant protein network modeler for newly sequenced species. Web server designed to instantly construct genome scale protein networks using protein sequence data. Provides network visualization, analysis pages and solution for instant network modeling of newly sequenced species. | protein network, protein, network, genome, sequence, pathway annotation, network visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Yonsei University; Seoul; South Korea |
National Research Foundation of Korea ; Next-Generation BioGreen 21 Program |
PMID:23685435 | Free, Freely available | OMICS_01548, biotools:jiffynet | https://bio.tools/jiffynet | SCR_011954 | 2026-02-16 09:48:04 | 1 | ||||||
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seq-annot Resource Report Resource Website 1+ mentions |
seq-annot (RRID:SCR_018731) | software application, software toolkit, standalone software, software resource | Software Python package for annotating and counting genomic features in genomes and metagenomes. Software tools to facilitate annotation and comparison of genomes and metagenomes. | Annotating, counting, comparison, genomic feature, genome, metagenome, metagenomics, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:seq-annot | https://bio.tools/seq-annot | SCR_018731 | 2026-02-16 09:49:31 | 1 | ||||||||
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TransDecoder Resource Report Resource Website 1000+ mentions |
TransDecoder (RRID:SCR_017647) | data processing software, software application, software resource, standalone software | Software tool to identify candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to genome using Tophat and Cufflinks.Starts from FASTA or GFF file. Can scan and retain open reading frames (ORFs) for homology to known proteins by using BlastP or Pfam search and incorporate results into obtained selection. Predictions can then be visualized by using genome browser such as IGV. | Identify, candidate, coding, region, transcript, sequence, de novo, RNAseq, assembly, alignment, genome, open, reading, frame, homology, protein, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:transDecoder, OMICS_10852 | https://bio.tools/TransDecoder https://sources.debian.org/src/transdecoder/ https://github.com/TransDecoder/TransDecoder/wiki |
SCR_017647 | , Find Coding Regions Within Transcripts | 2026-02-16 09:49:17 | 1309 | |||||||
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LACHESIS Resource Report Resource Website 50+ mentions |
LACHESIS (RRID:SCR_017644) | data processing software, software application, software resource | Software tool for chromosome scale scaffolding of de novo genome assemblies based on chromatin interactions.Method exploits signal of genomic proximity in Hi-C datasets for ultra long range scaffolding of de novo genome assemblies. | Chromosome, scale, scaffolding, de novo, genome, assembly, chromatin, Hi-C, data, clustering, contig | NHGRI HG006283; National Science Foundation ; NHGRI T32 HG000035 |
PMID:24185095 | Free, Available for download, Freely available | SCR_017644 | Ligating Adjacent Chromatin Enables Scaffolding In Situ | 2026-02-16 09:49:17 | 62 | ||||||||
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Purge_haplotigs Resource Report Resource Website 10+ mentions |
Purge_haplotigs (RRID:SCR_017616) | data processing software, software application, software resource | Pipeline for reassigning primary contigs that should be labelled as haplotigs. Used for third generation sequencing based assemblies to automate reassignment of allelic contigs, and to assist in manual curation of genome assemblies. | Reassigning, primary, contig, label, haplotig, third, generation, sequencing, assembly, allelic, curation, genome, alignment | PMID:30497373 | Free, Available for download, Freely available | SCR_017616 | 2026-02-16 09:49:16 | 14 | ||||||||||
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Recognition of Errors in Assemblies using Paired Reads Resource Report Resource Website 1+ mentions |
Recognition of Errors in Assemblies using Paired Reads (RRID:SCR_017625) | REAPR | data processing software, software application, software resource | Software tool to identify errors in genome assemblies without need for reference sequence. Can be used in any stage of assembly pipeline to automatically break incorrect scaffolds and flag other errors in assembly for manual inspection. Reports mis-assemblies and other warnings, and produces new broken assembly based on error calls. | Identify, error, genome, assembly, without, reference, sequence, incorrect, scaffold, error |
is listed by: Debian is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
European Union ; Wellcome Trust ; JSPS KAKENHI |
PMID:23710727 | Free, Available for download, Freely available | OMICS_04068 | https://sources.debian.org/src/reapr/ | SCR_017625 | 2026-02-16 09:49:17 | 2 | |||||
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JTK_CYCLE Resource Report Resource Website 1+ mentions |
JTK_CYCLE (RRID:SCR_017962) | data processing software, software application, software resource | Software R package for Detecting Rhythmic Components in Genome-Scale Data Sets. Non-parametric algorithm to identify rhythmic components in large datasets. Identifies and characterizes cycling variables in large datasets. | Washington University in St.Louis, detecting rhythmic, component, genome, scale, dataset, algorithm, non parametric, cycling, variable | NIMH P50 MH074924; NHBLI R01 HL097800; Pennsylvania Commonwealth Health Research Formula Funds |
PMID:20876817 | Free, Freely available | SCR_017962 | Jonckheere-Terpstra-Kendall-CYCLE | 2026-02-16 09:49:22 | 5 | ||||||||
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GeSeq Resource Report Resource Website 100+ mentions |
GeSeq (RRID:SCR_017336) | service resource, software application, software resource, data processing software | Software tool for rapid and accurate annotation of organelle genomes, in particular chloroplast genomes. | rapid, accurate, annotation, organelle, genome, chloroplast, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Human Frontier Science Program ; Max Planck Society ; German Science Foundation |
PMID:28486635 | Free, Freely available | biotools:geseq | https://bio.tools/geseq | SCR_017336 | 2026-02-16 09:49:13 | 375 | ||||||
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GeneSyntenyPipeline Resource Report Resource Website |
GeneSyntenyPipeline (RRID:SCR_018198) | data processing software, software application, software resource | Software pipeline was designed to draw gene synteny plot between genomes and obtain 1 to 1 gene pairs from each genome. | Genome, synteny, plot, JCVI, gene pair, data | Free, Available for download, Freely available | SCR_018198 | 2026-02-16 09:49:27 | 0 |
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