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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
ProbeMatchDB 2.0
 
Resource Report
Resource Website
ProbeMatchDB 2.0 (RRID:SCR_003433) ProbeMatchDB analysis service resource, data analysis service, data or information resource, database, production service resource, service resource Matches a list of microarray probes across different microrarray platforms (GeneChip, EST from different vendors, Operon Oligos) and species (human, mouse and rat), based on NCBI UniGene and HomoloGene. The capability to match protein sequence IDs has just been added to facilitate proteomic studies. The ProbeMatchDB is mainly used for the design of verification experiments or comparing the microarray results from different platforms. It can be used for finding equivalent EST clones in the Research Genetics sequence verified clone set based on results from Affymetirx GeneChips. It will also help to identify probes representing orthologous genes across human, mouse and rat on different microarray platforms. experiment, human, microarray, mouse, oligo, operon, platform, probe, protein, proteomic, rate, sequence, study, gene, est, cdna, sts marker, orthologous gene, ortholog, microarray probe, nucleotide sequence is related to: UniGene
is related to: HomoloGene
has parent organization: University of Michigan; Ann Arbor; USA
University of Michigan Microarray Network ;
Nancy Pritzker Depression Research Network ;
Department of Psychiatry pilot study ;
NIMH L99 MH60398;
NIDA R21 DA13754-01
PMID:11934751 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-33156 SCR_003433 2026-08-29 11:21:33 0
RINS
 
Resource Report
Resource Website
10+ mentions
RINS (RRID:SCR_003652) RINS software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. An intersection-based pathogen detection workflow that utilizes a user-provided custom reference genome set for identification of nonhuman sequences in deep sequencing datasets. This is a package recommended for advanced users only. virus, rna-seq, dna-seq, viral integration, clipped-sequence, paired-end, reconstruction, fusion transcript, sequence, perl is listed by: OMICtools
has parent organization: Stanford University School of Medicine; California; USA
PMID:22377895 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_00223 SCR_003652 2026-08-29 11:21:58 26
ChromasPro
 
Resource Report
Resource Website
10+ mentions
ChromasPro (RRID:SCR_000229) data acquisition software, data processing software, software application, software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31,2023. Software which is able to assemble data from 454 and Illumina next-generation sequencers, with up to 100,000 sequences if 2 Gb RAM is available. genome, sequence, dna, assemble, data, illumina, next gen sequence, next generation THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01808 SCR_000229 2026-08-29 11:20:21 14
Lasergene's SeqMan Pro
 
Resource Report
Resource Website
1+ mentions
Lasergene's SeqMan Pro (RRID:SCR_000283) data analysis software, data processing software, data visualization software, software application, software resource Software for analysis and DNA sequence assembly of Sanger data. It also provides visualizations and analysis of next-gen projects assembled by SeqMan NGen. dna, sequence, analysis, sanger, snp discovery, data visualization is listed by: OMICtools
works with: GenVision
Restricted OMICS_01810 SCR_000283 Lasergenes SeqMan Pro, SeqMan Pro, SeqMan Pro - Software for Contig Assembly and Analysis Including SNP Discovery Coverage Evaluation and Project Annotation, DANSEUR Lasergenes SeqMan Pro 2026-08-29 11:20:25 5
SPHINX
 
Resource Report
Resource Website
SPHINX (RRID:SCR_000534) SPHINX analysis service resource, data analysis service, production service resource, service resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Hybrid binning tool that achieves high binning efficiency by utilizing both "compositional" and "similarity" features of the query sequence during the binning process. SPHINX can analyze sequences in metagenomic data sets as rapidly as composition based approaches, but nevertheless has the accuracy and specificity of similarity based algorithms., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. metagenome, taxonomy, sequence, binning is listed by: OMICtools PMID:21030462 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01466 SCR_000534 2026-08-29 11:20:31 0
Ishtar
 
Resource Report
Resource Website
Ishtar (RRID:SCR_000538) software resource A program for designing primer pairs that amplify multiple target sequences using DNA thermodynamics and one class support vector machines. Written in Python. dna, thermodynamics, sequence, primer, pairs, loci, bioinformatics has parent organization: SourceForge Free, Available for download, Freely available, nlx_71525 SCR_000538 2026-08-29 11:20:31 0
Computational Cancer Genomics Group
 
Resource Report
Resource Website
1+ mentions
Computational Cancer Genomics Group (RRID:SCR_000772) data analysis software, data or information resource, data processing software, database, software application, software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Computational Cancer Genomics (CCG) group is dedicated to the development of analysis tools and databases relating molecular sequences and biological functions. Sponsors: This group is supported by the Swiss Institute of Bioinformatics (SIB). eukaryotic, expression, function, gene, analyzer, annotation, biological, clustering, computational, data, genome, in vitro, mapping, messengerrna, molecular, mpss, mrna, one-dimensional, organism, promoter, sage, sequence, snp, software, tag, technology, tool, transcription, transcriptome has parent organization: SIB Swiss Institute of Bioinformatics THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-25561 SCR_000772 CCG 2026-08-29 11:20:48 3
Cystic Fibrosis Mutation Database
 
Resource Report
Resource Website
10+ mentions
Cystic Fibrosis Mutation Database (RRID:SCR_000685) CFTR1, CFMDB data or information resource, data repository, database, service resource, storage service resource Collection of mutations in CFTR gene for international cystic fibrosis genetics research community. Provides up to date information about individual mutations in CFTR gene. All known CFTR mutations and sequence variants have been converted to standard nomenclature recommended by Human Genome Variation Society. On line process for submission of new mutations has been added.While they continue to ensure quality of data, they urge international community to give them feedback and suggestions. Clinical information in this database relates only to details of discovery of specific mutations. As part of 2010 upgrade, CFTR1 joined new project called CFTR2 - Clinical and Functional TRanslation of CFTR. Links to CFTR2 for many mutations in CFTR1 will provide up-to-date summaries of genotype-phenotype information from patient registries around the world. Gene, genetic, amino acid, clinical, cystic fibrosis, mutation, phenotype, genotype-phenotype, genotype, dna sequence, mouse, sequence, genetic variation, polymorphism, translation, function, sequence variation, metadata standard, cftr2, FASEB list is related to: CFTR2 Cystic fibrosis Free, Freely available nif-0000-21105, r3d100012093 https://doi.org/10.17616/R38356 SCR_000685 2026-08-29 11:20:34 42
DeNovoGear
 
Resource Report
Resource Website
1+ mentions
DeNovoGear (RRID:SCR_000670) software resource A software for detecting de novo mutations using sequencing data. It utilizes likelihood-based error modeling to reduce the false positive rate of mutative discovery in exome analysis. It also uses fragment information to identify the parental origin of germ-line mutations. de novo, mutation, sequence, dna, rna, error modeling, exome analysis is listed by: OMICtools
has parent organization: SourceForge
has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA
PMID:23975140 Free, Available for download, Freely available OMICS_00083 https://github.com/denovogear/denovogear SCR_000670 2026-08-29 11:20:34 3
MEGA
 
Resource Report
Resource Website
1000+ mentions
MEGA (RRID:SCR_000667) MEGA, MEGA6, MEGA4, MEGA 4, MEGA 11 data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit Software integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. Used for comparative analysis of DNA and protein sequences to infer molecular evolutionary patterns of genes, genomes, and species over time. MEGA version 4 expands on existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. MEGA version 6 enables inference of timetrees, as it implements RelTime method for estimating divergence times for all branching points in phylogeny. comparative, analysis, DNA, protein, sequence, molecular, evolution, pattern, gene, genome, evolution, FASEB list has parent organization: Pennsylvania State University Burroughs-Wellcome Fund ;
Japan Society for the Promotion of Science ;
NHGRI HG002096;
NHGRI HG006039;
NIGMS R01GM126567;
NIGMS R35GM139504;
NSF ABI 1661218
DOI:10.1093/molbev/msab120
PMID:24132122
PMID:31904846
PMID:22923298
PMID:21546353
PMID:17488738
PMID:15260895
PMID:11751241
PMID:8019868
Free, Available for download, Freely available SCR_023017, nlx_156838 https://www.megasoftware.net/mega4/ SCR_000667 MEGA11, Molecular Evolutionary Genetics Analysis, Molecular Evolutionary Genetics Analysis 6, Molecular Evolutionary Genetics Analysis 4 2026-08-29 11:20:44 2774
ProViDE
 
Resource Report
Resource Website
100+ mentions
ProViDE (RRID:SCR_004709) ProViDE software resource A similarity based binning algorithm that uses a customized set of alignment parameter thresholds / ranges, specifically suited for the accurate taxonomic labelling of viral metagenomic sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. metagenome, taxonomy, sequence, virus is listed by: OMICtools PMID:21544173 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01463 SCR_004709 ProViDE: Program for Viral Diversity Estimation, Program for Viral Diversity Estimation 2026-08-29 11:22:10 279
Repository of molecular brain neoplasia data
 
Resource Report
Resource Website
1+ mentions
Repository of molecular brain neoplasia data (RRID:SCR_004704) REMBRANDT analysis service resource, data analysis service, data or information resource, database, portal, production service resource, service resource, topical portal THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 28,2023. REMBRANDT is a data repository containing diverse types of molecular research and clinical trials data related to brain cancers, including gliomas, along with a wide variety of web-based analysis tools that readily facilitate the understanding of critical correlations among the different data types. REMBRANDT aims to be the access portal for a national molecular, genetic, and clinical database of several thousand primary brain tumors that is fully open and accessible to all investigators (including intramural and extramural researchers), as well as the public at-large. The main focus is to molecularly characterize a large number of adult and pediatric primary brain tumors and to correlate those data with extensive retrospective and prospective clinical data. Specific data types hosted here are gene expression profiles, real time PCR assays, CGH and SNP array information, sequencing data, tissue array results and images, proteomic profiles, and patients'''' response to various treatments. Clinical trials'''' information and protocols are also accessible. The data can be downloaded as raw files containing all the information gathered through the primary experiments or can be mined using the informatics support provided. This comprehensive brain tumor data portal will allow for easy ad hoc querying across multiple domains, thus allowing physician-scientists to make the right decisions during patient treatments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. gene, genetic, cancer, glioma, tumor, clinical genomics, functional genomics, clinical trial, genomics, gene expression, chromosomal aberration, clinical data, clinical, cellular pathway, gene ontology, molecule, brain, neoplasia, brain tumor, adult, pediatric, child, adolescent, gene expression profile, real time pcr assay, cgh array, snp array, sequence, tissue array, image, proteomic profile, treatment, protocol, molecular data, oncology, data mining, copy number array, gene expression array, secretion, kinase, membrane, gene-anomaly, translational research, personalized medicine, data integration, pathway, cell, phenotype is related to: Gene Ontology
is related to: Glioma Molecular Dignostic Initiatives
has parent organization: National Cancer Institute
Glioma, Brain cancer, Brain tumor NCI ;
NINDS
PMID:19208739 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-00230 SCR_004704 REMBRANDT (Repository of Molecular Brain Neoplasia Data), REMBRANDT - Repository of Molecular Brain Neoplasia Data, REpository for Molecular BRAin Neoplasia DaTa (REMBRANDT) 2026-08-29 11:22:10 2
AFTOL
 
Resource Report
Resource Website
10+ mentions
AFTOL (RRID:SCR_004650) AFTOL biospecimen repository, material storage repository, service resource, storage service resource THIS RESOURCE IS NO LONGER IN SERVICE, documented Jan 13, 2022; To enhance the understanding of the evolution of the Kingdom Fungi, 1500+ species were sampled for eight gene loci across all major fungal clades, plus a subset of taxa for a suite of morphological and ultrastructural characters with resulting data: AFTOL Molecular Database (generated by WASABI - Web Accessible Sequence Analysis for Biological Inference), Blast search the AFTOL Database (generated by WASABI), AFTOL primers (generated by WASABI), AFTOL primers by species (generated by WASABI), AFTOL alignments, and the AFTOL Structural and Biochemical Database. Users may submit samples to the AFTOL project. AFTOL is a collaboration centered around four universities in the United States: Duke University (Francois Lutzoni and Rytas Vilgalys), Clark University (David Hibbett), Oregon State University (Joey Spatafora), and University of Minnesota (David McLaughlin). Participants throughout the world have donated vouchers, taxon samples, and gene sequences. The aim of the project is to reconstruct the fungal tree of life using all available data for eight loci (nuclear ribosomal DNA: LSU, SSU, ITS (including 5.8s, ITS1 and ITS2); RNA polymerase II: RPB1, RPB2; elongation factor 1-alpha; mitochondrial SSU rDNA, and mitochondrial ATP synthase protein subunit 6). A further objective of this study is to summarize and integrate current knowledge regarding fungal subcellular features within this new phylogenetic framework. The name of the bioinformatic package developed for AFTOL is WASABI which provides an efficient communication platform to facilitate the collection and dissemination of molecular data to (and from) the laboratories and participants. All molecular data can be viewed, downloaded, verified, and corrected by the participants of AFTOL. A central goal of the WASABI interface is to establish an automated analysis framework that includes basecalling of newly generated chromatograms, contig assembly, quality verification of sequences (including a local BLAST), sequence alignment, and congruence test. Gene sequences that pass all tests and are finally verified by their authors will undergo automated phylogenetic analysis on a regular schedule. Although all steps are initially carried out noninteractively, the users can verify and correct the results at any step and thus initiate the reanalysis of dependent data. cytology, morphology, phylogeny, ultrastructure, primer, alignment, blast, sequence, taxonomy, structure, biochemical, subcellular, organism-related portal, data analysis service, culture, sporocarp, dna, pcr product, molecular, molecule, gene sequence has parent organization: Oregon State University; Oregon; USA NSF EF-0228671;
NSF 0090301
PMID:17486962
PMID:21652303
The community can contribute to this resource, THIS RESOURCE IS NO LONGER IN SERVICE nlx_64804 SCR_004650 Assembling the Fungal Tree of Life 2026-08-29 11:22:10 24
DiScRIBinATE
 
Resource Report
Resource Website
1+ mentions
DiScRIBinATE (RRID:SCR_004862) DiScRIBinATE software resource Software for accurate taxonomic classification of metagenomic sequences using a similarity based binning method. User needs to perform a similarity search of the input metagenomic sequences (reads) against the nr protein database using BLASTx search. The generated blastx output is then taken as the input by the DiScRIBinATE program. metagenome, classification, sequence is listed by: OMICtools PMID:21106121 Free for academic use, Non-commercial, Commercial use with permission, Acknowledgement requested, Copyright - Tata Consultancy Services OMICS_01453 SCR_004862 DiScRIBinATE: Distance Score Ratio for Improved Binning and Taxonomic Estimation, Distance Score Ratio for Improved Binning and Taxonomic Estimation 2026-08-29 11:22:02 4
MetaPhyler
 
Resource Report
Resource Website
10+ mentions
MetaPhyler (RRID:SCR_004848) software resource A taxonomic classifier for metagenomic shotgun reads, which uses phylogenetic marker genes as a taxonomic reference. The classifier, based on BLAST, uses different thresholds (automatically learned from the reference database) for each combination of taxonomic rank, reference gene, and sequence length. The reference database includes marker genes from all complete genomes, several draft genomes and the NCBI nr protein database. metagenome, classification, sequence, taxonomy, genome, microbiome, bio.tools is listed by: OMICtools
is listed by: Human Microbiome Project
is listed by: Debian
is listed by: bio.tools
has parent organization: University of Maryland; Maryland; USA
PMID:21989143 Acknowledgement requested, Available for download OMICS_01455, biotools:metaphyler https://bio.tools/metaphyler SCR_004848 MetaPhyler - Estimating Bacterial Composition from Metagenomic Sequences 2026-08-29 11:22:12 11
NCBI BLAST
 
Resource Report
Resource Website
10000+ mentions
NCBI BLAST (RRID:SCR_004870) BLAST data access protocol, data analysis software, data processing software, sequence analysis software, software application, software resource, web service Web search tool to find regions of similarity between biological sequences. Program compares nucleotide or protein sequences to sequence databases and calculates statistical significance. Used for identifying homologous sequences. genome, similarity, sequence, nucleotide, protein, gene, data, bio.tools is used by: MITE-Tracker
is used by: Cello2Go
is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is related to: G-BLASTN
is related to: genBlastA
has parent organization: NCBI
is required by: RelocaTE
works with: Whole Genome Shotgun (WGS) Project
works with: BLASTClust
works with: MOLE-BLAST
works with: Genotyping
National Library of Medicine PMID:16845079
PMID:18440982
Free, Freely available, Tutorial available OMICS_01436, nlx_84530, biotools:blast http://blast.ncbi.nlm.nih.gov, https://bio.tools/blast, https://sources.debian.org/src/ncbi-blast+/ SCR_004870 NCBI Basic Local Alignment Search Tool, NCBI BLAST, Basic Local Alignment Search Tool, BLAST 2026-08-29 11:22:02 17718
CHAoS
 
Resource Report
Resource Website
10+ mentions
CHAoS (RRID:SCR_005174) CHAoS software resource A Perl-based system for annotation of variants identified in high-throughput sequencing experiments. Functionality includes annotation of variants with information relating to population genetics, known transcripts, positional records, and sequence motif-based prediction. In addition, annotated variants can be summarized and extracted to facilitate downstream analysis. There is also basic support for gene-based biological annotation, and eventually will include tools for variant and genotype analysis and visualization. annotation, analysis, visualization, variant, high-throughput sequencing, perl, population genetic, transcript, positional record, sequence, motif, genotype is listed by: OMICtools
has parent organization: Wellcome Trust Centre for Human Genetics
GNU General Public License, v2 OMICS_00170 SCR_005174 chaos - Annotation analysis and visualization of variants from high-throughput sequencing experiments 2026-08-29 11:22:23 29
READSCAN
 
Resource Report
Resource Website
1+ mentions
READSCAN (RRID:SCR_005204) READSCAN software resource A highly scalable parallel software program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets. pathgen, genome, sequence, high-throughput sequence, align, read, host, microbe, virus, taxon, simulation, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: King Abdullah University of Science and Technology; Makkah Province; Saudi Arabia
PMID:23193222 OMICS_00222, biotools:readscan https://bio.tools/readscan SCR_005204 2026-08-29 11:22:24 5
PHAge Search Tool
 
Resource Report
Resource Website
100+ mentions
PHAge Search Tool (RRID:SCR_005184) PHAST analysis service resource, data analysis service, data or information resource, data set, production service resource, service resource A web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. It accepts either raw DNA sequence data or partially annotated GenBank formatted data and rapidly performs a number of database comparisons as well as phage cornerstone feature identification steps to locate, annotate and display prophage sequences and prophage features. Relative to other prophage identification tools, PHAST is up to 40 times faster and up to 15% more sensitive. It is also able to process and annotate both raw DNA sequence data and Genbank files, provide richly annotated tables on prophage features and prophage quality and distinguish between intact and incomplete prophage. PHAST also generates downloadable, high quality, interactive graphics that display all identified prophage components in both circular and linear genomic views. Databases available for download include Virus DB, Prophage and virus DB, Bacteria DB, and PHAST result DB. Pre-calculated genomes for viewing are also available. prophage sequence, genome, prophage, sequence, bacterial genome, plasmid, dna sequence, graph, phage, annotate, virus, nucleotide sequence, fasta, annotated genome, genbank, bio.tools, FASEB list is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: University of Alberta; Alberta; Canada
PMID:21672955 Acknowledgement requested biotools:phast, OMICS_00180 https://bio.tools/phast SCR_005184 PHAST - PHAge Search Tool 2026-08-29 11:22:09 243
MAFFT
 
Resource Report
Resource Website
10000+ mentions
MAFFT (RRID:SCR_011811) MAFFT alignment software, data processing software, image analysis software, software application, software resource, software toolkit Software package as multiple alignment program for amino acid or nucleotide sequences. Can align up to 500 sequences or maximum file size of 1 MB. First version of MAFFT used algorithm based on progressive alignment, in which sequences were clustered with help of Fast Fourier Transform. Subsequent versions have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and addition of new sequences to existing alignments. alignment, amino acid, nucleotide, sequence, DNA, sequence alignment, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
EMBL ;
Ministry of Education ;
Culture ;
Sports ;
Science and Technology of Japan
PMID:12136088
PMID:17118958
PMID:16362903
PMID:15661851
PMID:18439255
PMID:23023983
DOI:10.1093/bib/bbn013
biotools:MAFFT, OMICS_00979 https://www.ebi.ac.uk/Tools/msa/mafft/, https://www.genome.jp/tools-bin/mafft, https://myhits.isb-sib.ch/cgi-bin/mafft, https://bio.tools/MAFFT, https://sources.debian.org/src/mafft/ SCR_011811 Multiple Alignment using Fast Fourier Transform, MAFFT version 5, MAFFT version 7 2026-08-29 11:24:08 24687

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