Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
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.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
DNA From The Beginning: AN Animated Primer on the Basics of DNA, Genes, and Heredity Resource Report Resource Website |
DNA From The Beginning: AN Animated Primer on the Basics of DNA, Genes, and Heredity (RRID:SCR_008028) | DNAftB | video resource, narrative resource, training material, image collection, topical portal, portal, data or information resource | An animated primer on the basics of DNA, genes, and heredity organized around three key concepts: Classical Genetics, Molecules of Genetics, and Genetic Organization and Control. The science behind each concept is explained by: animation, image gallery, video interviews, problem, biographies, and links. | gene, genetic, chromosome, dna, heredity, human, protein, reverse transcriptase, transcription, translation, transposon, genetics, virus, rna, mutation | has parent organization: Cold Spring Harbor Laboratory | Josiah Macy Jr. Foundation | nif-0000-10208 | SCR_008028 | DNA from the Beginning | 2026-02-16 09:47:05 | 0 | |||||||
|
Velvet-SC Resource Report Resource Website 1+ mentions |
Velvet-SC (RRID:SCR_004377) | Velvet SC | software application, data processing software, sequence analysis software, data analysis software, software resource | Software package for short read data from single cells that improves assembly through use of progressively increasing coverage cutoff. Used for single cell Illumina sequences, allows variable coverage datasets to be utilized with assembly of E. coli and S. aureus single cell reads. Assembles single cell genome of uncultivated SAR324 clade of Deltaproteobacteria. | genome, single, cell, short, read, assembly |
is listed by: OMICtools is related to: Velvet has parent organization: University of California at San Diego; California; USA |
NHGRI R01 HG003647; Sloan Foundation ; NCRR P41 RR024851 |
PMID:21926975 | Free, Available for download, Freely available | OMICS_01504 | SCR_004377 | Velvet Single Cell | 2026-02-16 09:46:16 | 5 | |||||
|
MetaPhlAn Resource Report Resource Website 500+ mentions |
MetaPhlAn (RRID:SCR_004915) | software application, data processing software, data analysis resource, sequence analysis software, data analysis software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. It relies on unique clade-specific marker genes identified from reference genomes. | microbial community, microbial composition, microbial genome, microbial sequence |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian has parent organization: Bitbucket has parent organization: Harvard T.H. Chan School of Public Health |
PMID:22688413 DOI:10.1038/nmeth.3589 |
OMICS_02286 | http://huttenhower.sph.harvard.edu/metaphlan https://bitbucket.org/nsegata/metaphlan/ https://sources.debian.org/src/metaphlan2/ |
SCR_004915 | MetaPhlAn, Metagenomic Phylogenetic Analysis, MetaPhlAn version 2, MetaPhlAn - Metagenomic Phylogenetic Analysis, MetaPhlAn v2 | 2026-02-16 09:46:25 | 637 | |||||||
|
PHAge Search Tool Resource Report Resource Website 100+ mentions |
PHAge Search Tool (RRID:SCR_005184) | PHAST | data set, data analysis service, analysis service resource, production service resource, service resource, data or information 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 | 2026-02-16 09:46:26 | 225 | |||||
|
JGI Genome Portal Resource Report Resource Website 500+ mentions |
JGI Genome Portal (RRID:SCR_002383) | data or information resource, department portal, organization portal, portal | Portal providing access to all JGI genomic databases and analytical tools, sequencing projects and their status, search for and download assemblies and annotations of sequenced genomes, and interactively explore those genomes and compare them with other sequenced microbes, fungi, plants or metagenomes using specialized systems tailored to each particular class of organisms. The Department of Energy (DOE) Joint Genome Institute (JGI) is a national user facility with massive-scale DNA sequencing and analysis capabilities dedicated to advancing genomics for bioenergy and environmental applications. Beyond generating tens of trillions of DNA bases annually, the Institute develops and maintains data management systems and specialized analytical capabilities to manage and interpret complex genomic data sets, and to enable an expanding community of users around the world to analyze these data in different contexts over the web. | gene, computation, genome, genomics, model organism, assembly, annotation, sequenced genome, metagenome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: DOE Joint Genome Institute is parent organization of: Takifugu rubripes Genome |
Department of Energy | PMID:24225321 PMID:22110030 |
nif-0000-21230, SCR_004706, OMICS_01654, biotools:jgi_genome_portal, nlx_69965 | http://genome.jgi-psf.org https://bio.tools/jgi_genome_portal |
http://genome.jgi-psf.org/ | SCR_002383 | JGI Genome Portal, DOE Joint Genome Institute Genome Portal | 2026-02-16 09:45:44 | 865 | |||||
|
NBC Resource Report Resource Website 1+ mentions |
NBC (RRID:SCR_004772) | NBC | production service resource, service resource, data analysis service, analysis service resource | Webserver for taxonomic classification of metagenomic reads. | metagenome, genome, virus, taxonomy, next-generation sequencing, taxonomic classification, classification |
is listed by: OMICtools has parent organization: Drexel University; Pennsylvania; USA |
NSF DBI-0845827; DOE DE-SC0004335 |
PMID:1062764 PMID:19956701 |
OMICS_01458 | SCR_004772 | Naive Bayes Classification tool, Na����ve Bayesian Classification tool, Naive Bayesian Classification Tool | 2026-02-16 09:46:30 | 3 | ||||||
|
PRED-LIPO Resource Report Resource Website 10+ mentions |
PRED-LIPO (RRID:SCR_006187) | PRED-LIPO | production service resource, service resource, data analysis service, analysis service resource | A web tool using the Hidden Markov Model method for the prediction of lipoprotein signal peptides of Gram-positive bacteria, trained on a set of 67 experimentally verified lipoproteins. The method outperforms LipoP and the methods based on regular expression patterns, in various data sets containing experimentally characterized lipoproteins, secretory proteins, proteins with an N-terminal TM segment and cytoplasmic proteins. The method is also very sensitive and specific in the detection of secretory signal peptides and in terms of overall accuracy outperforms even SignalP, which is the top-scoring method for the prediction of signal peptides. | hidden markov model, lipoprotein signal peptide, gram-positive bacteria, lipoprotein, prediction, peptide, protein, signal peptide, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
National Scholarships Foundation of Greece | PMID:19367716 | Free | nlx_151732, biotools:pred-lipo | https://bio.tools/pred-lipo | SCR_006187 | PRED-LIPO: Prediction of Lipoprotein and Secretory Signal Peptides in Gram-positive Bacteria with Hidden Markov Models | 2026-02-16 09:46:43 | 17 | ||||
|
BacMap: Bacterial Genome Atlas Resource Report Resource Website 1+ mentions |
BacMap: Bacterial Genome Atlas (RRID:SCR_006988) | BacMap | data or information resource, database, atlas | An interactive visual database containing hundreds of fully labeled, zoomable, and searchable maps of bacterial genomes. It uses a visualization tool (CGView) to generate high-resolution circular genome maps from sequence feature information. Each map includes an interface that allows the image to be expanded and rotated. In the default view, identified genes are drawn to scale and colored according to coding directions. When a region of interest is expanded, gene labels are displayed. Each label is hyperlinked to a custom ''gene card'' which provides several fields of information concerning the corresponding DNA and protein sequences. Each genome map is searchable via a local BLAST search and a gene name/synonym search. A complete listing of the species and strains in the BacMap database is available on the BacMap homepage. Below each species/strain name is a list of the sequenced chromosomes and plasmids that are available. Some features of BacMap include: * Maps are available for 2023 bacterial chromosomes. * Each map supports zooming and rotation. * Map gene labels are hyperlinked to detailed textual annotations. * Maps can be explored manually, or with the help of BacMap''s built in text search and BLAST search. * A written synopsis of each bacterial species is provided. * Several charts illustrating the proteomic and genomic characteristics of each chromosome are available. * Flat file versions of the BacMap gene annotations, gene sequences and protein sequences can be downloaded. BacMap can be used to: * Obtain basic genome statistics. * Visualize the genomic context of genes. * Search for orthologues and paralogues in a genome of interest. * Search for conserved operon structure. * Look for gene content differences between bacterial species. * Obtain pre-calculated annotations for bacterial genes of interest. | gene, gene annotation, gene sequence, genome, bacteria, chromosome, protein sequence | has parent organization: University of Alberta; Alberta; Canada | Alberta Science Research Authority ; Western Economic Diversification ; Genome Canada ; Genome Prairie ; Western Economic Diversification Canada |
PMID:15608206 | Free, Acknowledgement requested | nif-0000-02591, r3d100012724 | https://doi.org/10.17616/R35502 | SCR_006988 | BacMap: An Interactive Atlas for Exploring Bacterial Genomes, BacMap genome atlas | 2026-02-16 09:46:51 | 4 | ||||
|
Mucosal HIV and Immunobiology Center Genetically-Defined Microbe Core Resource Report Resource Website |
Mucosal HIV and Immunobiology Center Genetically-Defined Microbe Core (RRID:SCR_015262) | service resource, core facility, access service resource, resource | Core composed of the Viral Unit, which provides labeled andn unlabeled viral components, and Bacterial Unit, which provides bacteria and bacterial proteins for research. The retroviral unit focues on the viral components of the retrovirus HIV-1. | microbe core, virology, retrovirus, hiv, aids, bacterial |
is listed by: NIDDK Information Network (dkNET) has parent organization: University of Alabama at Birmingham School of Medicine; Alabama; USA has parent organization: Mucosal HIV and Immunobiology Center is organization facet of: Mucosal HIV and Immunobiology Center |
Mucosal HIV | NIDDK DK064400 | Available to the DDRCC community | SCR_015262 | 2026-02-16 09:48:45 | 0 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on RRID then you can log in from here to get additional features in RRID such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
