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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
kraken2
 
Resource Report
Resource Website
1000+ mentions
kraken2 (RRID:SCR_026838) software application, software resource, source code Software tool as second version of Kraken taxonomic sequence classification system. taxonomic sequence classification system, taxonomic, sequence, classification system, NIGMS R01 GM118568;
NIGMS R35 GM130151;
NSF
PMID:31779668 Free, Available for download, Freely available SCR_026838 2026-08-29 11:34:50 1421
Fungal Genome Initiative
 
Resource Report
Resource Website
10+ mentions
Fungal Genome Initiative (RRID:SCR_003169) FGI data or information resource, data set Produces and analyzes sequence data from fungal organisms that are important to medicine, agriculture and industry. The FGI is a partnership between the Broad Institute and the wider fungal research community, with the selection of target genomes governed by a steering committee of fungal scientists. Organisms are selected for sequencing as part of a cohesive strategy that considers the value of data from each organism, given their role in basic research, health, agriculture and industry, as well as their value in comparative genomics. sequence, fungi, gene annotation, genome is listed by: 3DVC
has parent organization: Broad Institute
NHGRI ;
NSF ;
NIAID ;
USDA
Free, Freely available nif-0000-30591 SCR_003169 2026-08-29 11:31:53 18
University of Delaware Skate Genome Project
 
Resource Report
Resource Website
1+ mentions
University of Delaware Skate Genome Project (RRID:SCR_005300) Skate Genome Project access service resource, core facility, service resource Core facility provides a model for collaborative approaches to use specialized resources and expertise in an integrated process. Core builds on the expertise and resources provided by the Bioinformatics Cores of the five northeastern states that form NECC. The Skate Genome Annotation Workshops and Jamborees offer training and opportunities for faculty and students to work with and annotate genome sequences. Workshops include lectures, tutorials and exercises annotating the genome of the little skate, Leucoraja erinacea. skate, genome, genomics, bioinformatics, sequencing, annotate, sequence, workshop has parent organization: North East Cyberinfrastructure Consortium
has parent organization: University of Delaware; Delaware; USA
is parent organization of: SkateBase
Available to external user nlx_144349 SCR_005300 , University of Delaware, Genome Project, Skate 2026-08-29 11:32:01 1
SpliceDB
 
Resource Report
Resource Website
1+ mentions
SpliceDB (RRID:SCR_006262) SpliceDB data or information resource, data set Database of canonical and non-canonical mammalian splice sites. The information about verified splice site sequences for canonical and non-canonical sites is presented with the supporting evidence. Weight matrices were built for the major splice groups, which can be incorporated into gene prediction programs. gene, expressed sequence tag, splice, canonical, non-canonical, splice site, sequence, data set, splice site sequence is listed by: OMICtools
is listed by: 3DVC
is related to: GenBank
has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom
PMID:11125105
PMID:11058137
nlx_151853, OMICS_01892 http://linux1.softberry.com/berry.phtml?topic=splicedb http://genomic.sanger.ac.uk/spldb/SpliceDB.htm SCR_006262 SpliceDB: canonical and non-canonical splice site sequences in mammalian genes 2026-08-29 11:32:03 2
Fungi Sequencing Projects
 
Resource Report
Resource Website
1+ mentions
Fungi Sequencing Projects (RRID:SCR_008524) data or information resource, data set Fungal genomes available from the Sanger Institute. Data are accessible in a number of ways; for each organism there is a BLAST server, allowing search of the sequences. Sequences can also be down-loaded directly by FTP. In addition, for those organisms being sequenced using a cosmid approach, finished and annotated cosmids are submitted to EMBL and other public databases. genome, genomics, sequence, fungus, blast, data analysis service has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom nif-0000-30593 SCR_008524 Fungi Sequencing 2026-08-29 11:32:11 6
Yeast Resource Center
 
Resource Report
Resource Website
1+ mentions
Yeast Resource Center (RRID:SCR_007942) YRC biomedical technology research center, training resource Biomedical technology research center that (1) exploits the budding yeast Saccharomyces cerevisiae to develop novel technologies for investigating and characterizing protein function and protein structure (2) facilitates research and extension of new technologies through collaboration, and (3) actively disseminates data and technology to the research community. Through collaboration, the YRC freely provides resources and expertise in six core technology areas: Protein Tandem Mass Spectrometry, Protein Sequence-Function Relationships, Quantitative Phenotyping, Protein Structure Prediction and Design, Fluorescence Microscopy, Computational Biology. systems biology technology center, protein function, protein structure, mass spectrometry, protein, structure prediction, fluorescence microscopy, computational biology, sequence, function, phenotyping has parent organization: University of Washington; Seattle; USA NCRR ;
NIGMS P41 GM103533
nif-0000-03650 SCR_007942 YRC 2026-08-29 11:31:54 6
SkateBase
 
Resource Report
Resource Website
10+ mentions
SkateBase (RRID:SCR_005302) SkateBase analysis service resource, data analysis service, data or information resource, database, production service resource, service resource Portal supporting the North East Bioinformatics Collaborative''s project to sequence the genome of the Little Skate. Provided is a clearinghouse for Little Skate Genome Project and other publicly available Skate and Ray (Batoidea) genome data, and tools for data visualization and analysis. Little Skate Genome Project The little skate (Leucoraja erinacea) is a chondrichthyan (cartilaginous) fish native to the east coast of North America. Elasmobranchs (Skates, Rays, and Sharks) exhibit many fundamental vertebrate characteristics, including a neural crest, jaws and teeth, an adaptive immune system, and a pressurized circulatory system. These characteristics have been exploited to promote understanding about human physiology, immunology, stem cell biology, toxicology, neurobiology and regeneration. The development of standardized experimental protocols in elasmobranchs such as L. erinacea and the spiny dogfish shark (Squalus acanthias) has further positioned these organisms as important biomedical and developmental models. Despite this distinction, the only reported chondrichthyan genome is the low coverage (1.4x) draft genome of the elephant shark (Callorhinchus milii). To close the evolutionary gaps in available elasmobranch genome sequence data, and generate critical genomic resources for future biomedical study, the genome of L. erinacea is being sequenced by the North East Bioinformatics Collaborative (NEBC). As close evolutionary relatives, the little skate sequence will facilitate studies that employ dogfish shark and other elasmobranchs as model organisms. Skate tools include the SkateBLAST and the Skate Genome Browsers: Little Skate Mitochondrion, Thorny Skate Mitochondrion, and Ocellate Spot Skate Mitochondrion. little skate, leucoraja erinacea, sequence, genome, mitochondrion, thorny skate, ocellate spot skate, FASEB list has parent organization: North East Cyberinfrastructure Consortium
has parent organization: University of Delaware; Delaware; USA
has parent organization: University of Delaware Skate Genome Project
NIGMS 3P20GM103446-12S1 nlx_144350 SCR_005302 2026-08-29 11:22:18 40
SWEET-DB
 
Resource Report
Resource Website
1+ mentions
SWEET-DB (RRID:SCR_005324) SWEET, SWEET2 analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service Program that rapidly converts the primary sequence of a complex carbohydrate, as defined by standard nomenclature, directly into a reliable 3D molecular model by linking together preconstructed 3D molecular templates of monosaccharides in the manner specified by the sequence and then optimizing the 3D structure using the MM3 force field. The user interaction is supported by an input spreadsheet consisting of a grid of sugar symbol and connection type cells. Several ways to visualize and to output the generated structures and related information are implemented. carbohydrate, saccharide, 3d model, sequence, oligosaccharide, polysaccharide, 3d spatial image, carbohydrate sequence, modeling, carbohydrate modeling is related to: Distance Mapping
is related to: GlyProt
has parent organization: glycosciences.de
PMID:10498779 nif-0000-03520 http://www.dkfz-heidelberg.de/spec2/sweetdb/, http://www.glycosciences.de/sweetdb/ SCR_005324 SWEET II, Sweet-2 2026-08-29 11:22:19 2
LookSeq
 
Resource Report
Resource Website
1+ mentions
LookSeq (RRID:SCR_005625) LookSeq software resource A web-based application for alignment visualization, browsing and analysis of genome sequence data. alignment, visualization, browsing, analysis, genome, sequence is listed by: OMICtools
has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom
OMICS_00886 SCR_005625 2026-08-29 11:22:20 5
PeptideMapper
 
Resource Report
Resource Website
1+ mentions
PeptideMapper (RRID:SCR_005763) PeptideMapper data access protocol, software resource, web service The PeptideMapper Web-Service provides alignments of peptide sequence alignments to proteins, mRNA, EST, and HTC sequences from Genbank, RefSeq, UniProt, IPI, VEGA, EMBL, and HInvDb. This mapping infrastructure is supported, in part, by the compressed peptide sequence database infrastructure (Edwards, 2007) which enables a fast, suffix-tree based mapping of peptide sequences to gene identifiers and a gene-focused detailed mapping of peptide sequences to source sequence evidence. The PeptideMapper Web-Service can be used interactively or as a web-service using either HTTP or SOAP requests. Results of HTTP requests can be returned in a variety of formats, including XML, JSON, CSV, TSV, or XLS, and in some cases, GFF or BED; results of SOAP requests are returned as SOAP responses. The PeptideMapper Web-Service maps at most 20 peptides with length between 5 and 30 amino-acids in each request. The number of alignments returned, per peptide, gene, and sequence type, is set to 10 by default. The default can be changed on the interactive alignments search form or by using the max web-service parameter. peptide, sequence, protein, alignment, expressed sequence tag, mrna, est, htc, genbank, refseq, uniprot, ipi, vega, embl, hinvdb has parent organization: Edwards Lab NCI CA126189 PMID:17437027 nlx_149229 SCR_005763 PeptideMapper Web-Service, Peptide Mapper 2026-08-29 11:22:26 4
MolluscDB PartiGene database
 
Resource Report
Resource Website
1+ mentions
MolluscDB PartiGene database (RRID:SCR_006069) MolluscDB analysis service resource, data analysis service, data or information resource, database, production service resource, service resource A database housing EST information from nine mollusc species, including Lymnaea stagnalis, the pond snail. Co-curated with Angus davison of Nottingham University. lymnaea stagnalis, biomphalaria glabrata, mytilus galloprovincialis, mytilus edulis, argopecten irradians, crassostrea gigas, crassostrea virginica, dreissena polymorpha, sequence, blast, fasta, expressed sequence tag has parent organization: nematodes.org nlx_151475 SCR_006069 2026-08-29 11:22:30 2
DIG IT - Database of Immunoglobulins and Integrated Tools
 
Resource Report
Resource Website
1+ mentions
DIG IT - Database of Immunoglobulins and Integrated Tools (RRID:SCR_005924) DIG IT, DIGIT analysis service resource, data analysis service, data or information resource, database, production service resource, service resource The Database of Immunoglobulins and Integrated Tools (DIG IT) is an integrated resource storing sequences of annotated immunoglobulin variable domains of NCBI database and enriched with tools for searching and analyzing them. It contains 145759 heavy chain sequences and 71404 light chain sequences (47168 kappa type and 24236 lambda type) with assigned canonical structures for the hypervariable loops and the data on the type of antigen as well as the pairing information of immunoglobulin heavy and light chains (9672 total pairs). The user can input the immunoglobulin variable domain sequence (amino acid or nucleotide) of interest (heavy chain variable domain sequence; light chain variable domain sequence or both) to retrieve the closest sequences (sorted according to e-value) with complete annotation. The user can also directly query the database by antigen type, canonical structure, germline family in accordance to the requirements. sequence, immunoglobulin, variable domain, domain, heavy chain sequence, light chain sequence, antigen type, canonical structure, germline family, blast is related to: NCBI Nucleotide
is related to: NCBI Protein Database
has parent organization: Sapienza University of Rome; Rome; Italy
IIT SEED ;
King Abdullah University of Science and Technology KUK-I1-012-43;
Ministry of Health Contract Onc_Ord 25/07
PMID:22080506 The results obtained from the server shall be used for scientific purposes only, Excluding industrial or commercial purposes. Proper acknowledgement shall be made to the author of the server in publications resulting from the use of it. The results of the server shall not be made available to users outside the recipient''''s laboratory, Unless written consent is obtained. nlx_149625 http://www.biocomputing.it/ http://www.biocomputing.it/digit4/ SCR_005924 Database of Immunoglobulins and Integrated Tools, DIG IT! Database of Immunoglobulins and Integrated Tools, DIG IT! Database of Immunoglobulins with Integrated Tools, Database of Immunoglobulins Integrated Tools, DIG IT! Integrated Ig Database, DIG IT - Database of Immunoglobulins Integrated Tools 2026-08-29 11:22:27 1
ICEberg
 
Resource Report
Resource Website
50+ mentions
ICEberg (RRID:SCR_006026) ICEberg analysis service resource, data analysis service, data or information resource, database, production service resource, service resource ICEberg is an integrated database that provides comprehensive information about integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome. An ICE contains three typical modules, integration and excision, conjugation, and regulation modules, that collectively promote vertical inheritance and periodic lateral gene flow. Many ICEs carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. ICEberg offers a unique, highly organized, readily explorable archive of both predicted and experimentally supported ICE-relevant data. It currently contains details of 428 ICEs found in representatives of 124 bacterial species, and a collection of >400 directly related references. A broad range of similarity search, sequence alignment, genome context browser, phylogenetic and other functional analysis tools are readily accessible via ICEberg. ICEberg will facilitate efficient, multidisciplinary and innovative exploration of bacterial ICEs and be of particular interest to researchers in the broad fields of prokaryotic evolution, pathogenesis, biotechnology and metabolism. The ICEberg database will be maintained, updated and improved regularly to ensure its ongoing maximum utility to the research community. dna, protein, sequence, chromosome, element, gene, similarity search, sequence alignment, genome, phylogenetic, functional analysis, bio.tools, FASEB list is listed by: Debian
is listed by: bio.tools
has parent organization: Shanghai Jiao Tong University; Shanghai; China
National Natural Science Foundation of China 973 program 2009CB118901;
National Natural Science Foundation of China 973 program 2012CB721002;
National Natural Science Foundation of China 863 program 2011BAD23B05-3;
Ministry of Science and Technology China ;
Ministry of Education China NCET-10-0572;
Shanghai Jiaotong University ;
Shanghai Municipality ;
Action Medical Research SP4255;
Innovation Fellowship ;
East Midlands Development Agency
PMID:22009673 nlx_151424, biotools:iceberg https://bio.tools/iceberg SCR_006026 ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria 2026-08-29 11:22:29 89
HCV Sequence Database
 
Resource Report
Resource Website
10+ mentions
HCV Sequence Database (RRID:SCR_006019) HCV Sequence Database analysis service resource, data analysis service, data or information resource, database, production service resource, service resource The HCV sequence database collects and annotates sequence data and provides them to the public via a website that contains a user-friendly search interface and a large number of sequence analysis tools, based on the model of the highly regarded Los Alamos HIV database. The hepatitis C virus (HCV) is a significant threat to public health worldwide. The virus is highly variable and evolves rapidly, making it an elusive target for the immune system and for vaccine and drug design. At present, some 30 000 HCV sequences have been published. This central website provides annotated sequences and analysis tools that will be helpful to HCV scientists worldwide. Things you can do: * Find sequences in the database * Download sequences from the database * Retrieve data about the sequences * Analyze sequences * Work with the sequences using our tools * Download ready-made alignments The HCV sequence database was officially launched in September 2003. Since then, its usage has steadily increased and is now at an average of approximately 280 visits per day from distinct IP addresses. hepatitis c virus, sequence, annotation has parent organization: HCV Databases Hepatitis C NIAID PMID:15377502 Public nlx_151411 SCR_006019 Hepatitis C Sequence Database, Hepatitis C Virus Sequence Database, Los Alamos hepatitis C sequence database 2026-08-29 11:22:29 19
CMHD - Centre for Modeling Human Disease
 
Resource Report
Resource Website
10+ mentions
CMHD - Centre for Modeling Human Disease (RRID:SCR_006101) CMHD analysis service resource, biomaterial manufacture, data or information resource, database, material service resource, production service resource, service resource Multidisciplinary collaboration undertaking genome-wide mutagenesis to functionally annotate the mouse genome and develop new mouse models relevant to human disease. To achieve these goals two major research platforms are carried out: Gene trapping and ENU Mutagenesis. A new challenge is faced in the post-genomic era - the assignment of biological function to the human genome sequence and projecting that assignment into understanding of human health and disease. The Centre for Modeling Human Disease (CMHD) was established to take part in the worldwide initiative to address these challenges. At the CMHD, two fundamentally different, yet complimentary methods are employed to generate mutant mouse models of human disease: chemical mutagenesis by ethylnitrosourea (ENU), and gene trap insertional mutagenesis. The Centre contributes its resources to similar international efforts and is the first of its kind in Canada. The Center is also actively developing other mutagenic strategies including pharmacologic and genetic modifier screens to dissect disease pathways, and novel mutagenic techniques using embryonic stem cells. ENU Database * Statistics for Mouse Physiological Parameters * Search Mutants by Phenotype * Search Mutants by Heritability Gene Trap Database * Search by in vitro Expression Pattern * Search by Gene Trap Sequences CMHD Members Only (must register and login) * Search Mouse Line * Histopathology * Sperm, Tissue, Slide Archiving * CMHD Database Download CMHD Services * Phenotyping * Genetic Mapping * Pathology * Pathology Service Charges mutant, mouse model, chemical mutagenesis, ethylnitrosourea, gene trap insertion, mutagenesis, genome-wide mutagenesis, mouse genome, genome, phenotype, heritability, expression pattern, sequence, image, neurobiology, behavior, embryonic stem cell, gene trapping, enu mutagenesis, human disease has parent organization: Toronto Centre for Phenogenomics
is parent organization of: Centre for Modeling Human Disease Gene Trap Resource
Human disease CIHR ;
Genome Canada
Non-CMHD users are required to register and log in only if you wish to view images on our mouse models. nlx_151636 SCR_006101 Centre for Modeling Human Disease 2026-08-29 11:22:33 12
PRED-GPCR
 
Resource Report
Resource Website
1+ mentions
PRED-GPCR (RRID:SCR_006196) PRED-GPCR analysis service resource, data analysis service, data or information resource, data set, production service resource, service resource A prediction tool for GPCR Family Classification from sequence alone based on a probabilistic method that uses family-specific profile Hidden Markov Models. The PRED-GPCR system is based on a probabilistic method that uses family specific profile HMMs in order to determine to which GPCR family a query sequence belongs or resembles. The approach proposed in this method exploits the descriptive power of profile HMMs along with an exhaustive discrimination assessment method to select only highly selective and sensitive profiles, for each family. The collection of these profiles constitutes a signature library, which is scanned, for significant matches with a given query sequence. The output report for a query sequence consists of two sections: * A ranked list of the profile HMM matches, below the selected individual motif E-value cutoff, along with their corresponding family. * A ranked list of the Combined P-values, E-values as well as the number of profiles matched for each family. To cross-evaluate your results you can browse through Swiss-Prot, Trembl, Pfam and Prosite family related entries. g-protein coupled receptor, classification, hidden markov model, sequence, fasta, family classification, motif, bio.tools is listed by: Debian
is listed by: bio.tools
has parent organization: University of Athens Biophysics and Bioinformatics Laboratory
PMID:15215415 nlx_151741, biotools:pred-gpcr https://bio.tools/pred-gpcr SCR_006196 PRED-GPCR: GPCRs Family classification from sequence alone 2026-08-29 11:22:33 2
Generic Model Organism Database Project
 
Resource Report
Resource Website
1+ mentions
Generic Model Organism Database Project (RRID:SCR_001731) GMOD data or information resource, database, portal, software resource, topical portal A collection of open source software tools for creating and managing genome-scale biological databases. GMOD is made up databases, applications, and adaptor software that connects these components together. You can use it to create a small laboratory database of genome annotations, or a large web-accessible community database. At first GMOD just featured model organisms but now any organism with any kind of sequence associated with it is a good candidate as a subject for a GMOD database. There are GMOD databases with just protein sequence in them, with EST sequence only, those that are concerned primarily with gene expression, and even those dedicated to collections of RNA sequence. They have also heard of GMOD databases for oligonucleotides and plasmids. genome, biological database, model organism, software, annotation, gene, sequence, expressed sequence tag, gene expression, rna sequence, oligonucleotide, plasmid is related to: Generic GO Term Mapper
is related to: Generic GO Term Finder
has parent organization: USDA Agricultural Research Service
has parent organization: National Human Genome Research Institute
has parent organization: National Institute of General Medical Sciences
is parent organization of: SynView
is parent organization of: Apollo
is parent organization of: GBrowse
is parent organization of: CMAP
is parent organization of: GBrowse syn
Free, Freely Available nif-0000-10234 SCR_001731 Generic Model Organism Database 2026-08-29 11:20:49 7
BLASTX
 
Resource Report
Resource Website
10000+ mentions
BLASTX (RRID:SCR_001653) BLASTX analysis service resource, data analysis service, data or information resource, database, production service resource, service resource Web application to search protein databases using a translated nucleotide query. Translated BLAST services are useful when trying to find homologous proteins to a nucleotide coding region. Blastx compares translational products of the nucleotide query sequence to a protein database. Because blastx translates the query sequence in all six reading frames and provides combined significance statistics for hits to different frames, it is particularly useful when the reading frame of the query sequence is unknown or it contains errors that may lead to frame shifts or other coding errors. Thus blastx is often the first analysis performed with a newly determined nucleotide sequence and is used extensively in analyzing EST sequences. This search is more sensitive than nucleotide blast since the comparison is performed at the protein level. protein, translated nucleotide, blast, nucleotide, expressed sequence tag, sequence, genome, wgs, peptide, alignment, dna is listed by: OMICtools
is listed by: SoftCite
has parent organization: NCBI
PMID:28902395
PMID:8485583
Free, Freely Available nlx_153933, OMICS_00992 http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastx&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome SCR_001653 Translated BLAST, Translated BLAST: blastx 2026-08-29 11:20:47 10411
MACH 1.0
 
Resource Report
Resource Website
50+ mentions
MACH 1.0 (RRID:SCR_001759) data analysis software, data processing software, software application, software resource A Markov Chain based software tool for haplotyping, genotype imputation and disease association analysis that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals. gene, genetic, genomic, haplotype, genotype, genomic analysis, imaging genomics, imputation, snp, gene, haplotyping, sequence is listed by: OMICtools
is listed by: Genetic Analysis Software
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: Mach2dat
has parent organization: University of Michigan; Ann Arbor; USA
PMID:21058334
PMID:19715440
Free nlx_154202, OMICS_00064 SCR_001759 MArkov Chain Haplotyper MINIMAC, MArkov Chain Haplotyping 2026-08-29 11:21:06 58
Pecan
 
Resource Report
Resource Website
50+ mentions
Pecan (RRID:SCR_001909) software resource A Java consistency based multiple sequence alignment software program. java, sequence, alignment, consistency, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: University of California at Santa Cruz; California; USA
PMID:18849524 Free, Available for download, Freely available OMICS_03739, biotools:pecan http://hgwdev.cse.ucsc.edu/~benedict/code/Pecan.html, https://bio.tools/pecan SCR_001909 2026-08-29 11:20:54 51

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