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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Hypermut Resource Report Resource Website 100+ mentions |
Hypermut (RRID:SCR_014933) | sequence analysis software, software application, data processing software, web application, data analysis software, software resource | Web application for the analysis and detection of APOBEC-induced hypermutations. The first sequence in the input alignment will be used as the reference sequence, and each of the other sequences will be used as a query sequence. | mutation, hypermutation, sequence, sequence analysis software genome, web application | PMID:10869039 | SCR_014933 | Hypermut 2.0 | 2026-08-03 09:35:40 | 124 | ||||||||||
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Bowtie 2 Resource Report Resource Website 1000+ mentions |
Bowtie 2 (RRID:SCR_016368) | sequence analysis software, alignment software, software application, data processing software, data analysis software, image analysis software, software resource | Ultrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method. | sequence, analysis, long, reference, sequence, read, alignment, gap, local, pair, end, rna, rnaseq, bio.tools |
is used by: HLA-HD is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Bowtie |
NHGRI R01 HG006102; NIGMS R01 GM083873 |
PMID:22388286 | Free, Available for download, Freely available | biotools:bowtie2 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml, https://github.com/BenLangmead/bowtie2, https://bio.tools/bowtie2 | SCR_016368 | , bowtie 2, bowtie2 v 2.2.3 | 2026-08-03 09:35:35 | 1745 | |||||
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MacVector Resource Report Resource Website 1000+ mentions |
MacVector (RRID:SCR_015700) | sequence analysis software, software application, data processing software, data analysis software, software resource | Software application that provides sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, agarose gel simulation and a variety of other functions. | vector, sequence, sequence alignment, sequence editing, primer design, phylogenetic reconstruction, FASEB list | Commercially available, Available for purchase, Runs on Mac OS, Free version available | SCR_015700 | 2026-08-03 09:36:05 | 1496 | |||||||||||
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ALTER Resource Report Resource Website 100+ mentions |
ALTER (RRID:SCR_015968) | sequence analysis software, alignment software, software application, data processing software, web application, data analysis software, image analysis software, software resource | Web application to perform program-oriented conversion of DNA and protein alignments and transform between multiple sequence alignment formats. ALTER focuses on the specifications of mainstream alignment and analysis programs rather than on the conversion among more or less specific formats. | Alignment conversion, genome, sequence, DNA, protein, format alignment, phylogenetics, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
European Research Council ERC-2007-Stg 203161-PHYGENOM to D.P.; Spanish Ministry of Science and Education BFU2009-08611 to D.P.; Xunta de Galicia PGIDIT07PXIB310202PR to D.P.; INBIOMED initiative ; University of Vigo 09VIB10 to F.F-.R. |
PMID:20439312 DOI:10.1093/nar/gkq321 |
Freely available, Free, Available for download | OMICS_19786, biotools:alter | https://github.com/sing-group/ALTER, https://bio.tools/alter, https://sources.debian.org/src/alter-sequence-alignment/ | SCR_015968 | ALTER: ALignment Transformation EnviRonment, ALignment Transformation EnviRonment | 2026-08-03 09:36:15 | 112 | |||||
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AMAP Resource Report Resource Website 100+ mentions |
AMAP (RRID:SCR_015969) | alignment software, software application, data processing software, source code, image analysis software, software resource | Source code that performs multiple alignment of peptidic sequences. It utilizes posterior decoding and a sequence-annealing alignment, instead of the traditional progressive alignment method. | software, peptide, sequence, alignment, annealing, bioinformatics, multiple, svn, posterior, decoding |
is listed by: Debian is listed by: OMICtools has parent organization: University of California at Berkeley; Berkeley; USA |
NSF EF 03-31494; NHGRI R01 HG2362; NSF CCF0347992 |
PMID:17237099 DOI:10.1093/bioinformatics/btl311 |
Free, Available for download | OMICS_19787 | http://baboon.math.berkeley.edu/amap/, https://sources.debian.org/src/amap-align/ | https://sources.debian.org/src/amos-assembler/ | SCR_015969 | amap-align | 2026-08-03 09:36:31 | 388 | ||||
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Poretools Resource Report Resource Website 50+ mentions |
Poretools (RRID:SCR_015879) | sequence analysis software, software toolkit, software application, data processing software, data analysis software, software resource | Software toolkit for analyzing nanopore sequence data. | nanopore, sequence, python, oxford nanopore, MinION, quality control, downstream analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
Medical Research Council ; NHGRI R01 HG006693 |
PMID:25143291 | Open source, Free, Available for download | biotools:poretools | https://bio.tools/poretools | SCR_015879 | 2026-08-03 09:36:14 | 81 | ||||||
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Xenbase Resource Report Resource Website 100+ mentions |
Xenbase (RRID:SCR_003280) | XenBase | data repository, data or information resource, database, image repository, storage service resource, service resource | Data collection for Xenopus laevis and Xenopus tropicalis biology and genomics. | molecular neuroanatomy resource, dna target, protein target, gene, genome, function, sequence, orthology, publication, gene expression, model organism, genomics, development, annotation, blast, development stage, publication, in situ hybridization, immunohistochemistry, video resource, organism-related portal, experimental protocol, organism supplier, data analysis service, developmental stage, gold standard, bio.tools, FASEB list, RRID Community Authority |
is listed by: OMICtools is listed by: One Mind Biospecimen Bank Listing is listed by: bio.tools is listed by: Debian is related to: Bgee: dataBase for Gene Expression Evolution has parent organization: University of Calgary; Alberta; Canada is parent organization of: Xenopus Anatomy Ontology |
NICHD R01 HD045776; NICHD P41 HD064556 |
PMID:23125366 PMID:19884130 PMID:36755307 |
Free, Available for download, Freely available | biotools:xenbase, OMICS_01665, nif-0000-01286, r3d100010279 | http://www.xenbase.org/entry/, https://bio.tools/xenbase, https://doi.org/10.17616/R3MP4S | SCR_003280 | Xenbase: Xenopus laevis and tropicalis biology and genomics resource | 2026-08-03 09:32:13 | 446 | ||||
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ProbeMatchDB 2.0 Resource Report Resource Website |
ProbeMatchDB 2.0 (RRID:SCR_003433) | ProbeMatchDB | production service resource, data analysis service, data or information resource, database, analysis service resource, service resource | Matches a list of microarray probes across different microrarray platforms (GeneChip, EST from different vendors, Operon Oligos) and species (human, mouse and rat), based on NCBI UniGene and HomoloGene. The capability to match protein sequence IDs has just been added to facilitate proteomic studies. The ProbeMatchDB is mainly used for the design of verification experiments or comparing the microarray results from different platforms. It can be used for finding equivalent EST clones in the Research Genetics sequence verified clone set based on results from Affymetirx GeneChips. It will also help to identify probes representing orthologous genes across human, mouse and rat on different microarray platforms. | experiment, human, microarray, mouse, oligo, operon, platform, probe, protein, proteomic, rate, sequence, study, gene, est, cdna, sts marker, orthologous gene, ortholog, microarray probe, nucleotide sequence |
is related to: UniGene is related to: HomoloGene has parent organization: University of Michigan; Ann Arbor; USA |
University of Michigan Microarray Network ; Nancy Pritzker Depression Research Network ; Department of Psychiatry pilot study ; NIMH L99 MH60398; NIDA R21 DA13754-01 |
PMID:11934751 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33156 | SCR_003433 | 2026-08-03 09:32:07 | 0 | ||||||
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VIROME Resource Report Resource Website 10+ mentions |
VIROME (RRID:SCR_004362) | VIROME | production service resource, data analysis service, service resource, database, analysis service resource, data or information resource | A web-application designed for scientific exploration of metagenome sequence data collected from viral assemblages occurring within a number of different environmental contexts. The VIROME informatics pipeline focuses on the classification of predicted open-reading frames (ORFs) from viral metagenomes. The portal allows you to submit your viral metagenome to be processed through the VIROME analysis pipeline, and enable you to investigate your data via the VIROME user interface., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | open-reading frame, metagenome, virus, environment, sequence, library, genetic, polymorphism, orfan, environmental sequencing, shotgun metagenomics, viral ecology, function, taxonomy, peptide, blast |
is listed by: OMICtools is related to: UniRef is related to: CAMERA is related to: Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis has parent organization: University of Delaware; Delaware; USA has parent organization: University of Maryland School of Medicine; Maryland; USA |
Gordon and Betty Moore Foundation ; NSF award 0959894 |
PMID:23407591 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01506 | SCR_004362 | Viral Informatics Resource for Metagenome Exploration, Viral Informatics Resource for Metagenome Exploration - VIROME | 2026-08-03 09:32:25 | 22 | |||||
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SO Resource Report Resource Website 10+ mentions |
SO (RRID:SCR_004374) | SO | controlled vocabulary, data or information resource, ontology | A collaborative ontology for the definition of sequence features used in biological sequence annotation. SO was initially developed by the Gene Ontology Consortium. Contributors to SO include the GMOD community, model organism database groups such as WormBase, FlyBase, Mouse Genome Informatics group, and institutes such as the Sanger Institute and the EBI. Input to SO is welcomed from the sequence annotation community. The OBO revision is available here: http://sourceforge.net/p/song/svn/HEAD/tree/ SO includes different kinds of features which can be located on the sequence. Biological features are those which are defined by their disposition to be involved in a biological process. Biomaterial features are those which are intended for use in an experiment such as aptamer and PCR_product. There are also experimental features which are the result of an experiment. SO also provides a rich set of attributes to describe these features such as polycistronic and maternally imprinted. The Sequence Ontologies use the OBO flat file format specification version 1.2, developed by the Gene Ontology Consortium. The ontology is also available in OWL from Open Biomedical Ontologies. This is updated nightly and may be slightly out of sync with the current obo file. An OWL version of the ontology is also available. The resolvable URI for the current version of SO is http://purl.obolibrary.org/obo/so.owl. | annotation, sequence, biological sequence, sequence variation, genome, genome annotation, owl, FASEB list |
is listed by: BioPortal is related to: ASOoViR is related to: VAGrENT has parent organization: OBO has parent organization: Gene Ontology |
NHGRI HG02273 | PMID:20796305 PMID:20226267 PMID:18629179 PMID:15892872 |
The community can contribute to this resource | nlx_38918 | SCR_004374 | Sequence Ontology Project, Sequence Types and Features Ontology, Sequence Ontology | 2026-08-03 09:32:30 | 44 | |||||
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Repository of molecular brain neoplasia data Resource Report Resource Website 1+ mentions |
Repository of molecular brain neoplasia data (RRID:SCR_004704) | REMBRANDT | portal, production service resource, data analysis service, service resource, database, topical portal, analysis service resource, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 28,2023. REMBRANDT is a data repository containing diverse types of molecular research and clinical trials data related to brain cancers, including gliomas, along with a wide variety of web-based analysis tools that readily facilitate the understanding of critical correlations among the different data types. REMBRANDT aims to be the access portal for a national molecular, genetic, and clinical database of several thousand primary brain tumors that is fully open and accessible to all investigators (including intramural and extramural researchers), as well as the public at-large. The main focus is to molecularly characterize a large number of adult and pediatric primary brain tumors and to correlate those data with extensive retrospective and prospective clinical data. Specific data types hosted here are gene expression profiles, real time PCR assays, CGH and SNP array information, sequencing data, tissue array results and images, proteomic profiles, and patients'''' response to various treatments. Clinical trials'''' information and protocols are also accessible. The data can be downloaded as raw files containing all the information gathered through the primary experiments or can be mined using the informatics support provided. This comprehensive brain tumor data portal will allow for easy ad hoc querying across multiple domains, thus allowing physician-scientists to make the right decisions during patient treatments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, cancer, glioma, tumor, clinical genomics, functional genomics, clinical trial, genomics, gene expression, chromosomal aberration, clinical data, clinical, cellular pathway, gene ontology, molecule, brain, neoplasia, brain tumor, adult, pediatric, child, adolescent, gene expression profile, real time pcr assay, cgh array, snp array, sequence, tissue array, image, proteomic profile, treatment, protocol, molecular data, oncology, data mining, copy number array, gene expression array, secretion, kinase, membrane, gene-anomaly, translational research, personalized medicine, data integration, pathway, cell, phenotype |
is related to: Gene Ontology is related to: Glioma Molecular Dignostic Initiatives has parent organization: National Cancer Institute |
Glioma, Brain cancer, Brain tumor | NCI ; NINDS |
PMID:19208739 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00230 | SCR_004704 | REMBRANDT (Repository of Molecular Brain Neoplasia Data), REMBRANDT - Repository of Molecular Brain Neoplasia Data, REpository for Molecular BRAin Neoplasia DaTa (REMBRANDT) | 2026-08-03 09:32:42 | 2 | ||||
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NCBI BLAST Resource Report Resource Website 10000+ mentions |
NCBI BLAST (RRID:SCR_004870) | BLAST | sequence analysis software, web service, software application, data processing software, data analysis software, data access protocol, software resource | Web search tool to find regions of similarity between biological sequences. Program compares nucleotide or protein sequences to sequence databases and calculates statistical significance. Used for identifying homologous sequences. | genome, similarity, sequence, nucleotide, protein, gene, data, bio.tools |
is used by: MITE-Tracker is used by: Cello2Go is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: G-BLASTN is related to: genBlastA has parent organization: NCBI is required by: RelocaTE works with: Whole Genome Shotgun (WGS) Project works with: BLASTClust works with: MOLE-BLAST works with: Genotyping |
National Library of Medicine | PMID:16845079 PMID:18440982 |
Free, Freely available, Tutorial available | OMICS_01436, nlx_84530, biotools:blast | http://blast.ncbi.nlm.nih.gov, https://bio.tools/blast, https://sources.debian.org/src/ncbi-blast+/ | SCR_004870 | NCBI Basic Local Alignment Search Tool, NCBI BLAST, Basic Local Alignment Search Tool, BLAST | 2026-08-03 09:32:44 | 15381 | ||||
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AFTOL Resource Report Resource Website 10+ mentions |
AFTOL (RRID:SCR_004650) | AFTOL | service resource, biospecimen repository, material storage repository, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented Jan 13, 2022; To enhance the understanding of the evolution of the Kingdom Fungi, 1500+ species were sampled for eight gene loci across all major fungal clades, plus a subset of taxa for a suite of morphological and ultrastructural characters with resulting data: AFTOL Molecular Database (generated by WASABI - Web Accessible Sequence Analysis for Biological Inference), Blast search the AFTOL Database (generated by WASABI), AFTOL primers (generated by WASABI), AFTOL primers by species (generated by WASABI), AFTOL alignments, and the AFTOL Structural and Biochemical Database. Users may submit samples to the AFTOL project. AFTOL is a collaboration centered around four universities in the United States: Duke University (Francois Lutzoni and Rytas Vilgalys), Clark University (David Hibbett), Oregon State University (Joey Spatafora), and University of Minnesota (David McLaughlin). Participants throughout the world have donated vouchers, taxon samples, and gene sequences. The aim of the project is to reconstruct the fungal tree of life using all available data for eight loci (nuclear ribosomal DNA: LSU, SSU, ITS (including 5.8s, ITS1 and ITS2); RNA polymerase II: RPB1, RPB2; elongation factor 1-alpha; mitochondrial SSU rDNA, and mitochondrial ATP synthase protein subunit 6). A further objective of this study is to summarize and integrate current knowledge regarding fungal subcellular features within this new phylogenetic framework. The name of the bioinformatic package developed for AFTOL is WASABI which provides an efficient communication platform to facilitate the collection and dissemination of molecular data to (and from) the laboratories and participants. All molecular data can be viewed, downloaded, verified, and corrected by the participants of AFTOL. A central goal of the WASABI interface is to establish an automated analysis framework that includes basecalling of newly generated chromatograms, contig assembly, quality verification of sequences (including a local BLAST), sequence alignment, and congruence test. Gene sequences that pass all tests and are finally verified by their authors will undergo automated phylogenetic analysis on a regular schedule. Although all steps are initially carried out noninteractively, the users can verify and correct the results at any step and thus initiate the reanalysis of dependent data. | cytology, morphology, phylogeny, ultrastructure, primer, alignment, blast, sequence, taxonomy, structure, biochemical, subcellular, organism-related portal, data analysis service, culture, sporocarp, dna, pcr product, molecular, molecule, gene sequence | has parent organization: Oregon State University; Oregon; USA | NSF EF-0228671; NSF 0090301 |
PMID:17486962 PMID:21652303 |
The community can contribute to this resource, THIS RESOURCE IS NO LONGER IN SERVICE | nlx_64804 | SCR_004650 | Assembling the Fungal Tree of Life | 2026-08-03 09:32:42 | 22 | |||||
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PHAge Search Tool Resource Report Resource Website 100+ mentions |
PHAge Search Tool (RRID:SCR_005184) | PHAST | production service resource, data analysis service, data or information resource, analysis service resource, service resource, data set | A web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. It accepts either raw DNA sequence data or partially annotated GenBank formatted data and rapidly performs a number of database comparisons as well as phage cornerstone feature identification steps to locate, annotate and display prophage sequences and prophage features. Relative to other prophage identification tools, PHAST is up to 40 times faster and up to 15% more sensitive. It is also able to process and annotate both raw DNA sequence data and Genbank files, provide richly annotated tables on prophage features and prophage quality and distinguish between intact and incomplete prophage. PHAST also generates downloadable, high quality, interactive graphics that display all identified prophage components in both circular and linear genomic views. Databases available for download include Virus DB, Prophage and virus DB, Bacteria DB, and PHAST result DB. Pre-calculated genomes for viewing are also available. | prophage sequence, genome, prophage, sequence, bacterial genome, plasmid, dna sequence, graph, phage, annotate, virus, nucleotide sequence, fasta, annotated genome, genbank, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Alberta; Alberta; Canada |
PMID:21672955 | Acknowledgement requested | biotools:phast, OMICS_00180 | https://bio.tools/phast | SCR_005184 | PHAST - PHAge Search Tool | 2026-08-03 09:32:48 | 225 | |||||
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SkateBase Resource Report Resource Website 10+ mentions |
SkateBase (RRID:SCR_005302) | SkateBase | production service resource, data analysis service, service resource, database, analysis service resource, data or information 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 | 2026-08-03 09:32:49 | 40 | ||||||||
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SWEET-DB Resource Report Resource Website 1+ mentions |
SWEET-DB (RRID:SCR_005324) | SWEET, SWEET2 | production service resource, data analysis service, web service, analysis service resource, data access protocol, service resource, software resource | 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 | 2026-08-03 09:32:39 | 2 | ||||||
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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 | production service resource, data analysis service, service resource, database, analysis service resource, data or information 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 | 2026-08-03 09:32:50 | 1 | |||
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PeptideMapper Resource Report Resource Website 1+ mentions |
PeptideMapper (RRID:SCR_005763) | PeptideMapper | web service, data access protocol, software resource | 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 | 2026-08-03 09:32:55 | 4 | ||||||
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Princeton High Throughput Sequencing and Microarray Facility Resource Report Resource Website |
Princeton High Throughput Sequencing and Microarray Facility (RRID:SCR_012619) | Princeton High Throughput Sequencing and Microarray Facility, High Throughput Sequencing and Microarray Facility | production service resource, data analysis service, access service resource, analysis service resource, service resource, core facility | Core facility provides researchers with access to high-throughput sequencing technologies. The staff provide consultation on experimental design, library preparation, and data analysis. The Sequencing Core Facility works closely with Bioinformatics staff in the Center for Quantitative Biology to provide researchers with computing power and consulting services to analyze sequencing data. | sequence, microarray, data analysis, analysis, consulting, |
is listed by: ScienceExchange is related to: Princeton University Labs and Facilities has parent organization: Princeton University; New Jersey; USA |
Available to External User | SciEx_567 | SCR_012619 | High Throughput Sequencing, Microarray, Princeton University, Facility | 2026-08-03 09:34:59 | 0 | |||||||
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Human Genome Project Information Resource Report Resource Website 50+ mentions |
Human Genome Project Information (RRID:SCR_013028) | video resource, portal, slide, narrative resource, funding resource, topical portal, data or information resource, training material | This resource gives information about the U.S. Human Genome Project, which was was a 13-year effort to to discover all the estimated 20,000-25,000 human genes and make them accessible for further biological study. The primary project goals were to: - identify all the approximately 20,000-25,000 genes in human DNA, - determine the sequences of the 3 billion chemical base pairs that make up human DNA, - store this information in databases, - improve tools for data analysis, - transfer related technologies to the private sector, and - address the ethical, legal, and social issues (ELSI) that may arise from the project. To help achieve these goals, researchers also studied the genetic makeup of several nonhuman organisms. These include the common human gut bacterium Escherichia coli, the fruit fly, and the laboratory mouse. These parallel studies helped to develop technology and interpret human gene function. Sponsors: The DOE Human Genome Program and the NIH National Human Genome Research Institute (NHGRI) together sponsored the U.S. Human Genome Project. | escherichia coli, fruit fly, function, gene, genome, genetic, bacterium, base pair, biological, dna, human, mouse, sequence, FASEB list |
has parent organization: National Institutes of Health has parent organization: United States Department of Energy |
nif-0000-10252 | SCR_013028 | HGP | 2026-08-03 09:35:17 | 59 |
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