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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.

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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Website Status Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
BEBaC
 
Resource Report
Resource Website
BEBaC (RRID:SCR_000621) BEBaC software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for Bayesian estimation of bacterial communities. linux, bayesian is listed by: OMICtools
has parent organization: University of Helsinki; Helsinki; Finland
PMID:22406836 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01440 SCR_000621 Bayesian estimation of bacterial communities 2026-02-14 01:59:46 0
BSRD
 
Resource Report
Resource Website
10+ mentions
BSRD (RRID:SCR_004249) BSRD data repository, storage service resource, data or information resource, service resource, database A repository for bacterial small regulatory RNA. They welcome you to submit new experimental validated sRNA targets. srna target, srna, small regulatory non-coding rna, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: Chinese University of Hong Kong; Hong Kong; China
PMID:23203879 Acknowledgement requested, The community can contribute to this resource biotools:bsrd, OMICS_01533 https://bio.tools/bsrd SCR_004249 BSRD - Bacterial Small Regulatory RNA Database, Bacterial Small Regulatory RNA Database 2026-02-14 02:00:42 29
Genomes Online Database
 
Resource Report
Resource Website
100+ mentions
Genomes Online Database (RRID:SCR_002817) GOLD data repository, storage service resource, data or information resource, service resource, database Database of information regarding genome and metagenome sequencing projects, and their associated metadata, around the world. It also provides information related to organism properties such as phenotype, ecotype and disease. Both complete and ongoing projects, along with their associated metadata, can be accessed. Users can also register, annotate and publish genome and metagenome data. genome, genetics, metagenome, biosample, phenotype, ecotype, disease, sequencing, FASEB list is listed by: re3data.org
has parent organization: DOE Joint Genome Institute
PMID:22135293
PMID:19914934
PMID:17981842
PMID:16381880
PMID:11125068
PMID:10498782
Free, Freely available, Available for download r3d100010808, nif-0000-02918 https://doi.org/10.17616/R39310 SCR_002817 Genomes On Line Database (GOLD), GOLD:Genomes Online Database 2026-02-14 02:00:33 159
National Center for Marine Algae and Microbiota
 
Resource Report
Resource Website
50+ mentions
National Center for Marine Algae and Microbiota (RRID:SCR_002120) NCMA biomaterial supply resource, organism supplier, material resource National marine phytoplankton collection, maintaining over 2700 strains from around the world, most are marine phytoplankton but they also have benthic, macrophytic, freshwater and heterotrophic organisms - now incorporating bacteria and viruses. Strain records have (when available): * collection and isolation information * culturing medium recipes and growth conditions * photographs * GenBank accession link * collection site map * link to the taxonomic database Micro*scope The deposition of new strains are welcome if the strains are a valuable addition to the collection. Examples include strains that are referred to in publications, contain interesting molecular, biochemical or physiological properties, are the basis for taxonomic descriptions, are important for aquaculture, or are from an unusual geographical location or ecological habitat. The NCMA offers a course in phytoplankton culturing techniques and facilities for visiting scientists are available at the new laboratories in East Boothbay, Maine. Services include: Mass Culturing DNA and RNA, Purification, Private Holdings, Culture Techniques Course, Visiting Scientists, Single Cell Genomics, Flow Cytometry, Corporate Alliances and Technology Transfer. marine phytoplankton, marine, phytoplankton, virus, benthic, macrophytic, freshwater, heterotrophic, microbiota, seawater, FASEB list is listed by: One Mind Biospecimen Bank Listing
is listed by: CINERGI
NSF Restricted nlx_154729 SCR_002120 Provasoli-Guillard National Center for Culture of Marine Phytoplankton, Provasoli-Guillard National Center for Marine Algae and Microbiota, CCMP 2026-02-14 02:00:18 53
Protein Lounge
 
Resource Report
Resource Website
10+ mentions
Protein Lounge (RRID:SCR_002117) ProteinLounge data analysis service, analysis service resource, data or information resource, production service resource, service resource, narrative resource, training material, database Complete siRNA target database, complete Peptide-Antigen target database and a Kinase-Phosphatase database. They have also developed the largest database of illustrated signal transduction pathways, which are interconnected to their extensive protein database and online gene / protein analysis tools. The interactive web-based databases and software help life-scientists understand the complexity of systems biology. Systems biology efforts focus on understanding cellular networks, protein interactions involved in cell signaling, mechanisms of cell survival and apoptosis leading to development or identification of drug candidates against a variety of diseases. In the post-genomic era, one of the major concerns for life-science researchers is the organization of gene / protein data. Protein Lounge has met this concern by organizing all necessary data about genes / proteins into one portal. gene, antigen, bioinformatics, kinase, life science, peptide, phosphatase, signal transduction pathway, sirna, systems biology, protein, biology, cellular network, protein interaction, cell signaling, cell survival, apoptosis, peptide-antigen, kinase-phosphatase, image, pathway Restricted nif-0000-20903 SCR_002117 Protein Lounge - Redefining Biology 2026-02-14 02:00:15 29
NCBI Genome
 
Resource Report
Resource Website
500+ mentions
NCBI Genome (RRID:SCR_002474) Genome data repository, storage service resource, data or information resource, service resource, database Database that organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations in six major organism groups: Archaea, Bacteria, Eukaryotes, Viruses, Viroids, and Plasmids. Genomes of over 1,200 organisms can be found in this database, representing both completely sequenced organisms and those for which sequencing is in progress. Users can browse by organism, and view genome maps and protein clusters. Links to other prokaryotic and archaeal genome projects, as well as BLAST tools and access to the rest of the NCBI online resources are available. chromosome, organelle, plasmid, viroid, virus, genome, sequence, map, assembly, annotation, gene mapping, dna, blast, protein cluster, gold standard is listed by: re3data.org
is related to: MapViewer
is related to: UniProt Proteomes
is related to: CaspBase
has parent organization: NCBI
Free, Freely avaialble nif-0000-02802, r3d100010785 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome
https://doi.org/10.17616/R3R89S
SCR_002474 Entrez Genomes, Entrez Genome, NCBI, Genome, Genome Database, Genome: Information by genome sequence 2026-02-14 02:00:17 577
Microsens
 
Resource Report
Resource Website
Microsens (RRID:SCR_003906) Microsens commercial organization Commercial organization specializing in bacterial detection including tuberculosis, therapeutic protein and protein aggregation diseases. * Tools for rapid and simple bacteria and virus extraction including tuberculosis * Seprion technology for the detection and study of protein aggregates and protein aggregation diseases * LiMA technology for the ultra sensitive detection of bacteria and bacterial contamination virus, protein aggregate, protein, therapeutic protein is related to: Predict-TB Tuberculosis, Protein aggregation disease nlx_158251 SCR_003906 Microsens Diagnostics Ltd., Microsens Medtech Ltd, Microsens Medtech, Microsens Medtech Ltd. 2026-02-14 02:00:38 0
ATCC
 
Resource Report
Resource Website
10000+ mentions
ATCC (RRID:SCR_001672) ATCC commercial organization Global nonprofit biological resource center (BRC) and research organization that provides biological products, technical services and educational programs to private industry, government and academic organizations. Its mission is to acquire, authenticate, preserve, develop and distribute biological materials, information, technology, intellectual property and standards for the advancement and application of scientific knowledge. The primary purpose of ATCC is to use its resources and experience as a BRC to become the world leader in standard biological reference materials management, intellectual property resource management and translational research as applied to biomaterial development, standardization and certification. ATCC characterizes cell lines, bacteria, viruses, fungi and protozoa, as well as develops and evaluates assays and techniques for validating research resources and preserving and distributing biological materials to the public and private sector research communities. biomaterial, cell line, culture, microorganism, proteomics, protozoa, tissue, bacteria, virus, fungus, standardization, molecular genomics, reagent, yeast, microbial culture, stem cell, dna, FASEB list is used by: NIA Mouse cDNA Project Home Page
is used by: NIF Data Federation
is listed by: One Mind Biospecimen Bank Listing
is related to: Cell Line Knowledge Base
is related to: Vector Database
is related to: Hyper Cell Line Database
is related to: BEI Resource Repository
is related to: NCBI BioSample
is related to: Xenopus Gene Collection
is related to: Mammalian Gene Collection
is related to: Zebrafish Gene Collection
is related to: Integrated Cell Lines
is related to: ATCC STR database
is parent organization of: Mantle Cell Lymphoma Cell Bank
works with: Cellosaurus
Free, Freely Available ISNI: 0000 0001 2161 7948, Wikidata: Q2843042, grid.281196.5, nif-0000-10159 https://ror.org/03thhhv76 SCR_001672 ATCC: The Global Bioresource Center, American Type Culture Collection, ATCC(dna), ATCC(in host) 2026-02-14 02:00:08 106406
Ensembl Genomes
 
Resource Report
Resource Website
100+ mentions
Ensembl Genomes (RRID:SCR_006773) web service, data or information resource, data access protocol, software resource, database Database portal offering integrated access to genome-scale data from non-vertebrate species of scientific interest, developed using the Ensembl genome annotation and visualization platform. Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. Many of the databases supporting the portal have been built in close collaboration with the scientific community - essential for maintaining the accuracy and usefulness of the resource. A common set of user interfaces (which include a graphical genome browser, FTP, BLAST search, a query optimized data warehouse, programmatic access, and a Perl API) is provided for all domains. Data types incorporated include annotation of (protein and non-protein coding) genes, cross references to external resources, and high throughput experimental data (e.g. data from large scale studies of gene expression and polymorphism visualized in their genomic context). Additionally, extensive comparative analysis has been performed, both within defined clades and across the wider taxonomy, and sequence alignments and gene trees resulting from this can be accessed through the site. genome, gold standard, bio.tools, FASEB list is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: Ensembl
is related to: Ensembl
is related to: g:Profiler
has parent organization: European Bioinformatics Institute
European Molecular Biology Laboratory ;
European Union FELICS 021902 (RII3);
BBSRC BB/F019793/1
PMID:24163254
PMID:19884133
r3d100011197, OMICS_01648, nlx_65207, biotools:ensembl_genomes https://bio.tools/ensembl_genomes
https://doi.org/10.17616/R3MW6M
SCR_006773 Ensembl Genomes: Extending Ensembl across the taxonomic space, EnsemblGenomes, Ensembl Genome 2026-02-14 02:01:23 276
Psort
 
Resource Report
Resource Website
100+ mentions
Psort (RRID:SCR_007038) PSORT data processing software, data analysis service, portal, analysis service resource, data set, data or information resource, production service resource, data analysis software, service resource, software application, software resource, topical portal Portal to the PSORT family of computer programs for the prediction of protein localization sites in cells, as well as other datasets and resources relevant to localization prediction. The standalone versions are available for download for larger analyses. subcellular, localization, prediction, gram, gram-positive, gram-negative, sequence, fasta, protein, protein localization, cell, motif, profile, amino acid, subcellular localization is listed by: OMICtools
is related to: PSORT II
has parent organization: Simon Fraser University; British Columbia; Canada
OMICS_01634, nif-0000-31883 http://psort.hgc.jp/ SCR_007038 Psort.org, PSORT: Prediction of Protein Sorting Signals and Localization Sites in Amino Acid Sequences 2026-02-14 02:01:17 209
Pathogenic Disease Ontology
 
Resource Report
Resource Website
Pathogenic Disease Ontology (RRID:SCR_010405) PDO data or information resource, ontology, controlled vocabulary An ontology for describing both human infectious disease caused by bacteria and the disease that is related to bacterial infection. owl is listed by: BioPortal Infectious disease, (caused by bacteria), Bacterial infection related disease nlx_157543 SCR_010405 2026-02-14 02:01:57 0
OMPdb
 
Resource Report
Resource Website
OMPdb (RRID:SCR_006221) OMPdb data analysis service, analysis service resource, data or information resource, production service resource, service resource, database A database of Beta-barrel outer membrane proteins from Gram-negative bacteria. The web interface of OMPdb offers the user the ability not only to view the available data, but also to submit advanced queries for text search within the database''s protein entries or run BLAST searches against the database. The most up-to-date version of the database (as well as all past versions) can be downloaded in various formats (flat text, XML format or raw FASTA sequences). For constructing OMPdb, multiple freely accessible resources were combined and a detailed literature search was performed. The classification of OMPdb''s protein entries into families is based mainly on structural and functional criteria. Information included in the database consists of sequence data, as well as annotation for structural characteristics (such as the transmembrane segments), literature references and links to other public databases, features that are unique worldwide. Along with the database, a collection of profile Hidden Markov Models that were shown to be characteristic for Beta-barrel outer membrane proteins was also compiled. This set, when used in combination with our previously developed algorithms (PRED-TMBB, MCMBB and ConBBPRED) will serve as a powerful tool in matters of discrimination and classification of novel Beta-barrel proteins and whole-genome analyses., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. beta-barrel, outer membrane protein, gram-negative bacteria, protein, protein sequence, transmembrane, annotation, genome-wide analyses, comparative genomics, sequence, structure, blast, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: University of Athens Biophysics and Bioinformatics Laboratory
PMID:20952406 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01611, biotools:ompdb, nlx_151768 https://bio.tools/ompdb SCR_006221 OMPdb - A database of Beta-barrel outer membrane proteins from Gram-negative bacteria 2026-02-14 02:01:14 0
VAAL
 
Resource Report
Resource Website
VAAL (RRID:SCR_001184) VAAL software resource A polymorphism discovery algorithm for short reads. To run it, you provide reads (and quality scores) from a "sample genome" as input, along with a vector sequence to trim from the reads, and a reference sequence for a related genome to compare to. VAAL produces as output a an assembly for the sample genome, together with a mask showing which bases are "trusted". It then deduces from that a list of differences between the sample and related genomes. Alternatively, it can be provided as input read data for two sample genomes, together with a reference sequence for a related genome. In this case, VAAL produces assemblies for each of the sample genomes, and compares them to each other, thereby deducing a list of differences between them. VAAL has been tested on bacteria, using single lanes of 36 bp unpaired reads from the Illumina platform. Note: This software package is no longer supported and information on this page is provided for archival purposes only. dna sequence, polymorphism, parallel sequencing, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Broad Institute
PMID:19079253 biotools:vaal, OMICS_02170 https://bio.tools/vaal SCR_001184 2026-02-14 02:00:01 0
NCBI Assembly Archive Viewer
 
Resource Report
Resource Website
100+ mentions
NCBI Assembly Archive Viewer (RRID:SCR_012917) NCBI Assembly Archive Viewer data repository, storage service resource, data set, data or information resource, service resource Database providing information on structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data. The Archive links the raw sequence information found in the Trace Archive with assembly information found in publicly available sequence repositories (GenBank/EMBL/DDBJ). sequence alignment, sequence chromatogram, assembly, virus is recommended by: NIDDK Information Network (dkNET)
is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases
is listed by: OMICtools
is related to: GenBank
is related to: Trace Archive
is related to: DNA DataBank of Japan (DDBJ)
is related to: European Nucleotide Archive (ENA)
OMICS_00890, r3d100012688 http://www.ncbi.nlm.nih.gov/assembly
https://doi.org/10.17616/R31NJMA8
http://www.ncbi.nlm.nih.gov/Traces/assembly/assmbrowser.cgi SCR_012917 Assembly Archive Viewer, NCBI Assembly, Assembly 2026-02-14 02:02:44 274
Ribosomal Database Project
 
Resource Report
Resource Website
1000+ mentions
Ribosomal Database Project (RRID:SCR_006633) RDP data or information resource, database, resource A database which provides ribosome related data services to the scientific community, including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences. It specifically contains information on quality-controlled, aligned and annotated bacterial and archaean 16S rRNA sequences, fungal 28S rRNA sequences, and a suite of analysis tools for the scientific community. Most of the RDP tools are now available as open source packages for users to incorporate in their local workflow. microbiome, database, rrna gene sequence, rrna, ribosome, genome browser, high-throughput sequencing, bacteria, archaea, fungi, FASEB list is listed by: OMICtools
is listed by: Human Microbiome Project
has parent organization: Michigan State University; Michigan; USA
is parent organization of: RDPipeline
DOE DE-FG02-99ER62848;
DOE DE-SC0004601;
DOE DE-FC02-07ER64494;
NIEHS P42 ES004911;
NSF DBI-0328255;
USDA 2008-35107-04542;
NHLBI U01HL098961;
NIDDK UH3 DK083993
PMID:24288368
PMID:17586664
Open source r3d100012372, nif-0000-03404, OMICS_01513 https://doi.org/10.17616/R3C087 SCR_006633 Ribosomal Database Project 2026-02-14 02:01:20 1441
cpnDB: A Chaperonin Database
 
Resource Report
Resource Website
1+ mentions
cpnDB: A Chaperonin Database (RRID:SCR_002263) cpnDB data analysis service, analysis service resource, data or information resource, production service resource, service resource, database A curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The database contains all available sequences for both group I and group II chaperonins. Users can search the database by Chaperonin type, group (I or II), BLAST, or other options, and can also enter and analyze FASTA sequences. chaperonin sequence, microbial ecology, phylogenetics, chaperonin, plastid, mitochondria, cytoplasm, sequence, blast, fasta, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
Canadian Biotechnology Strategy ;
National Research Council Genomics and Health Initiative
PMID:15289485 Free, Freely available biotools:cpndb, OMICS_01511, nif-0000-02694 https://bio.tools/cpndb http://www.cpndb.ca/cpnDB/home.php SCR_002263 2026-02-14 02:04:28 3
Pathosystems Resource Integration Center
 
Resource Report
Resource Website
1000+ mentions
Pathosystems Resource Integration Center (RRID:SCR_004154) PATRIC data analysis service, analysis service resource, data or information resource, production service resource, service resource, bioinformatics resource center, database A Bioinformatics Resource Center bacterial bioinformatics database and analysis resource that provides researchers with an online resource that stores and integrates a variety of data types (e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data) and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. The PATRIC project includes three primary collaborators: the University of Chicago, the University of Manchester, and New City Media. The University of Chicago is providing genome annotations and a PATRIC end-user genome annotation service using their Rapid Annotation using Subsystem Technology (RAST) system. The National Centre for Text Mining (NaCTeM) at the University of Manchester is providing literature-based text mining capability and service. New City Media is providing assistance in website interface development. An FTP server and download tool are available. genomics, genome, transcriptomics, protein-protein interaction, sequence typing, proteobacteria, brucella, rickettsia, coxiella, coronavirus, calicivirus, lyssavirus, virus, hepatitis a, hepatitis e, pathway, proteome, metabolic pathway, drug, vaccine, diagnostics, FASEB list is listed by: OMICtools
has parent organization: Virginia Polytechnic Institute and State University; Virginia; USA
NIAID PMID:24225323
PMID:17142235
Free, Public, Acknowledgement requested r3d100010142, OMICS_01658, nlx_17476 http://patricbrc.vbi.vt.edu/portal/portal/patric/Home
https://doi.org/10.17616/R3WS3X
http://patric.vbi.vt.edu/ SCR_004154 PathoSystems Resource Integration Center, PATRIC, Pathosystems Resource Integration Center 2026-02-14 02:04:52 1083
xFITOM
 
Resource Report
Resource Website
1+ mentions
xFITOM (RRID:SCR_014445) sequence analysis software, data processing software, data analysis software, software application, software resource, standalone software A fully customizable program that uses a graphical user interface to locate transcription factor-binding sites in genomic sequences. xFITOM scans DNA or RNA sequences for putative binding sites as defined by a collection of aligned known sites, a consensus sequence in IUPAC degenerate-base format, or a combination of the two. transcription factor, binding site, information theory, customizable program, sequence analysis software uses: GenBank
is related to: CollecTF
PMID:21346861 Available for download, Acknowledgement requested http://www.mybiosoftware.com/fitom-1-0-detection-binding-sites-dna-rna-sequences.html compbio.umbc.edu/Software/xFITOM/ http://research.umbc.edu/~erill/ SCR_014445 2026-02-14 02:04:32 7
OrthoVenn2
 
Resource Report
Resource Website
100+ mentions
OrthoVenn2 (RRID:SCR_022504) data access protocol, software resource, web service Web server for whole genome comparison and annotation of orthologous clusters across multiple species.Works on any operating system with modern browser and Javascript enabled. Used to identify orthologous gene clusters and supports user define species to upload customized protein sequences. Interactive graphic tool which provides Venn diagram view for comparing multiple species protein sequences. whole genome comparison and annotation, orthologous clusters across multiple species, identify orthologous gene clusters, comparing multiple species protein sequences National Natural Science Foundation of China PMID:31053848 Free, Freely available SCR_022504 2026-02-14 02:04:56 255
CW-PRED
 
Resource Report
Resource Website
10+ mentions
CW-PRED (RRID:SCR_006188) CW-PRED data analysis service, production service resource, service resource, analysis service resource A web tool for the prediction of Cell Wall-Anchored Proteins in Gram+ Bacteria. Gram-positive bacteria have surface proteins that are often implicated in virulence. A group of extracellular proteins attached to the cell wall contains an LPXTG-like motif that is target for cleavage and covalent coupling to peptidoglycan by sortase enzymes. A new Hidden Markov Model (HMM), an extension to the HMM model from Litou et al., http://www.ncbi.nlm.nih.gov/pubmed/18464329, was developed for predicting the LPXTG and LPXTG-like cell-wall proteins of Gram-positive bacteria. An analysis of 177 completely sequenced genomes has been performed as well. We identified in total 1456 cell-wall proteins, from which 1283 have the LPXTG motif, 39 the NPXTG motif, 53 have the LPXTA and 81 the LAXTG motif. hidden markov model, gram-positive bacteria, protein, classification, cell-wall protein has parent organization: University of Athens Biophysics and Bioinformatics Laboratory Free for academic use, Acknowledgement requested nlx_151733 SCR_006188 CW-PRED: A HMM-based method for the classification of cell wall-anchored proteins of Gram-positive bacteria 2026-02-14 02:05:54 16

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