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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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University of Delaware Skate Genome Project Resource Report Resource Website 1+ mentions |
University of Delaware Skate Genome Project (RRID:SCR_005300) | Skate Genome Project | service resource, access service resource, core facility | 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 | 2026-08-03 09:32:51 | 1 | |||||||
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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 | 2026-08-03 09:33:50 | 6 | |||||||||
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Yeast Resource Center Resource Report Resource Website 1+ mentions |
Yeast Resource Center (RRID:SCR_007942) | YRC | training resource, biomedical technology research center | 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 | 2026-08-03 09:33:36 | 6 | |||||||
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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 | 2026-08-03 09:32:57 | 2 | |||||
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kraken2 Resource Report Resource Website 1000+ mentions |
kraken2 (RRID:SCR_026838) | software resource, software application, source code | Software tool as second version of Kraken taxonomic sequence classification system. | taxonomic sequence classification system, taxonomic, sequence, classification system, | NSF ; NIGMS R01 GM118568; NIGMS R35 GM130151 |
PMID:31779668 | Free, Available for download, Freely available | SCR_026838 | 2026-08-03 09:39:01 | 1107 | |||||||||
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SCANDAN-DICOM-labelling Resource Report Resource Website |
SCANDAN-DICOM-labelling (RRID:SCR_028365) | software application, source code, text extraction software, text-mining software, software resource | Software tool for rules for DICOM tag based labelling. Regular expression used during the SCANDAN project to label MRI scans based on DICOM tag. | sequence, MRI, DICOM standard, Text-mining algorithm, Brain | DOI:10.1101/2025.10.21.25338469 | Free, Available for download, Freely available | SCR_028365 | 2026-08-03 09:39:41 | 0 | ||||||||||
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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 | 2026-08-01 12:02:06 | 50 | |||||||
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PolyPhred Resource Report Resource Website 100+ mentions |
PolyPhred (RRID:SCR_002337) | PolyPhred | software resource | Software program that compares fluorescence-based sequences across traces obtained from different individuals to identify heterozygous sites for single nucleotide substitutions. Its functions are integrated with the use of three other programs: Phred (Brent Ewing and Phil Green), Phrap (Phil Green), and Consed (David Gordon and Phil Green). PolyPhred identifies potential heterozygotes using the base calls and peak information provided by Phred and the sequence alignments provided by Phrap. Potential heterozygotes identified by PolyPhred are marked for rapid inspection using the Consed tool. | windows, sequence, nucleotide substitution, heterozygote, polymorphic, genotype, single nucleotide polymorphism, fluorescence, single nucleotide substitution, polymorphism, insertion, deletion, indel, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA |
PMID:17115056 PMID:16493422 PMID:9207020 |
Free for academic use, Commercial use requires a license | biotools:polyphred, OMICS_01815 | https://bio.tools/polyphred | SCR_002337 | 2026-08-01 12:01:46 | 123 | ||||||
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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 | 2026-08-01 12:02:44 | 279 | ||||||
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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 | 2026-08-01 12:02:48 | 4 | ||||||
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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 | 2026-08-01 12:02:45 | 11 | ||||||
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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 | 2026-08-01 12:02:32 | 26 | |||||||
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MedBlast Resource Report Resource Website 1+ mentions |
MedBlast (RRID:SCR_008202) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. An algorithm that finds articles most relevant to a genetic sequence. In the genomic era, researchers often want to know more information about a biological sequence by retrieving its related articles. However, there is no available tool yet to achieve conveniently this goal. Here, a new literature-mining tool MedBlast is developed, which uses natural language processing techniques, to retrieve the related articles of a given sequence. An online server of this program is also provided. The genome sequencing projects generate such a large amount of data every day that many molecular biologists often encounter some sequences that they know nothing about. Literature is usually the principal resource of such information. It is relatively easy to mine the articles cited by the sequence annotation; however, it is a difficult task to retrieve those relevant articles without direct citation relationship. The related articles are those described in the given sequence (gene/protein), or its redundant sequences, or the close homologs in various species. They can be divided into two classes: direct references, which include those either cited by the sequence annotation or citing the sequence in its text; indirect references, those which contain gene symbols of the given sequence. A few additional issues make the task even more complicated: (1) symbols may have aliases; and (2) one sequence may have a couple of relatives that we want to take into account too, which include redundant (e.g. protein and gene sequences) and close homologs. Here the issues are addressed by the development of the software MedBlast, which can retrieve the related articles of the given sequence automatically. MedBlast uses BLAST to extend homology relationships, precompiled species-specific thesauruses, a useful semantics technique in natural language processing (NLP), to extend alias relationship, and EUtilities toolset to search and retrieve corresponding articles of each sequence from PubMed. MedBlast take a sequence in FASTA format as input. The program first uses BLAST to search the GenBank nucleic acid and protein non-redundant (nr) databases, to extend to those homologous and corresponding nucleic acid and protein sequences. Users can input the BLAST results directly, but it is recommended to input the result of both protein and nucleic acid nr databases. The hits with low e-values are chosen as the relatives because the low similarity hits often do not contain specific information. Very long sequences, e.g. 100k, which are usually genomic sequences, are discarded too, for they do not contain specific direct references. User can adjust these parameters to meet their own needs. | gene, article, biological, data, genome, genomic, homolog, literature, medline interfaces, mining, molecular, protein, sequence, specie | National Natural Science Foundation of China 39990600-03; Knowledge Innovation Program of the Chinese Academy of Sciences KSCX2-2-07; Knowledge Innovation Program of the Chinese Academy of Sciences KJCX1-08 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21253 | SCR_008202 | MedBlast | 2026-08-01 12:03:28 | 1 | ||||||||
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Joint Center for Structural Genomics Resource Report Resource Website 50+ mentions |
Joint Center for Structural Genomics (RRID:SCR_008251) | JCSG | institution | The JCSG is a multi-institutional consortium that aims to explore the expanding protein universe to find new challenges and opportunities to significantly contribute to new biology, chemistry and medicine through development of HT approaches to structural genomics. The mission of JCSG is to to operate a robust HT protein structure determination pipeline as a large-scale production center for PSI-2. A major goal is to ensure that innovative high-throughput approaches are developed that advance not only structural genomics, but also structural biology in general, via investigation of large numbers of high-value structures that populate protein fold and family space and by increasing the efficiency of structure determination at substantially reduced cost. The JCSG centralizes each core activity into single dedicated sites, each handling distinct, but interconnected objectives. This unique approach allows each specialized group to focus on its own area of expertise and provides well-defined interfaces among the groups. In addition, this approach addresses the requirements for the scalability needed to process large numbers of targets at a greatly reduced cost per target. JCSG production groups are: - Administrative Core - Bioinformatics Core - Crystallomics Core - Structure Determination Core - NMR Core JCSG is deeply committed to the development of new technologies that facilitate high throughput structural genomics. The areas of development include hardware, software, new experimental methods, and adaptation of existing technologies to advance genome research. In the hardware arena, their commitment is to the development of technologies that accelerate structure solution by increasing throughput rates at every stage of the production pipeline. Therefore, one major area of hardware development has been the implementation of robotics. In the software arena, they have developed enterprise resource software that track success, failures, and sample histories from target selection to PDB deposition, annotation and target management tools, and helper applications aimed at facilitating and automating multiple steps in the pipeline. Sponsors: The Joint Center for Structural Genomics is funded by the National Institute of General Medical Sciences (NIGMS), as part of the second phase of the Protein Structure Initiative (PSI) of the National Institutes of Health (U54 GM074898). | exclusion chromatography, expression, fine-structure spectroscopy, fold, absorption, affinity, bacterial, baculovirus, bioinformatics, biology, biophysical, cell, chemistry, cloning, crystallization, crystallomics, differential scanning calorimetry, diffraction, domain, genomic, gnfuge, growth, hardware, ief gel electrophoresis, macromoleuclar, medicine, microexpression, mouse, nmr, optical density, physicochemical, protein, purification, recombinatorial, robotics, sds-page, sequence, software, structural, structural biology, structure, technology, thermocycler, topoisomerase, tryptic mass spectrometry, uv/vis absorbance scan, x-ray |
has parent organization: University of California at San Diego; California; USA has parent organization: Scripps Research Institute has parent organization: Sanford Burnham Prebys Medical Discovery Institute has parent organization: Stanford University; Stanford; California |
nif-0000-22295, grid.419677.a | https://ror.org/00exr1241 | SCR_008251 | JCSG | 2026-08-01 12:03:28 | 99 | |||||||
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Affymetrix Power Tools Resource Report Resource Website 10+ mentions |
Affymetrix Power Tools (RRID:SCR_008401) | software resource | Affymetrix Power Tools (APT) are a set of cross-platform command line programs that implement algorithms for analyzing and working with Affymetrix GeneChip arrays. APT programs are intended for power users who prefer programs that can be utilized in scripting environments and are sophisticated enough to handle the complexity of extra features and functionality. APT provides platform for developing and deploying new algorithms without waiting for the GUI implementations. This resource is supported by Affymetrix, Inc. | Affymetrix, Inc., Genomics, Clinical, Study, Bioinformatic, Windows, MacOS, Linux, resource, Data, Normalization, Sequence, Annotation, Gene, Expression, Pattern, Motif, Inference, Toolkit, Model, Fitting, Algorithm |
has parent organization: Affymetrix has parent organization: Affymetrix |
nif-0000-30070 | https://www.affymetrix.com/support/developer/powertools/changelog/install.html, https://media.affymetrix.com/support/developer/powertools/changelog/index.html | http://www.affymetrix.com/partners_programs/programs/developer/tools/powertools.affx | SCR_008401 | APT | 2026-08-01 12:03:52 | 30 | |||||||
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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 | 2026-08-01 12:02:47 | 26 | |||||||
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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 | 2026-08-01 12:02:47 | 5 | |||||||
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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 | 2026-08-01 12:03:00 | 5 | |||||||||
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GASiC Resource Report Resource Website 1+ mentions |
GASiC (RRID:SCR_006765) | GASiC | software resource | A method to correct read alignment results for the ambiguities imposed by similarities of genomes. | metagenome, genome, sequence, python |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:22941661 DOI:10.1093/nar/gks803 |
BSD License | OMICS_01437 | https://sources.debian.org/src/gasic/ | SCR_006765 | GASiC - Genome Abundance Similarity Correction, Genome Abundance Similarity Correction | 2026-08-01 12:03:16 | 3 | |||||
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CD-HIT-OTU Resource Report Resource Website 50+ mentions |
CD-HIT-OTU (RRID:SCR_006983) | CD-HIT-OTU | software resource | Data analysis service and software program that perform Operantional Taxonomic Units (OTUs) finding. It uses a three-step clustering for identifying OTUs. The first-step clustering is raw read filtering and trimming. The second step is error-free reads picking.. At the last step, OTU clustering is done at different distanct cutoffs (0.01, 0.02, 0.03... 0.12). | 454, read, illumina, rrna, fasta, metagenome, sequence, clustering, metagenomics, next-generation sequencing, protein |
is listed by: OMICtools has parent organization: CD-HIT |
PMID:22772836 PMID:21899761 |
GNU General Public License, v2, Acknowledgement requested | OMICS_01441 | SCR_006983 | 2026-08-01 12:03:21 | 88 |
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