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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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skewer Resource Report Resource Website 10+ mentions |
skewer (RRID:SCR_001151) | skewer | software resource, data processing software, software application | Software program for adapter trimming that is specially designed for processing Illumina paired-end sequences. | illumina, unix/linux, c++, adapter trimming, paired-end, sequence, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:24925680 | Free, Available for download, Freely available | OMICS_02106, biotools:skewer | https://bio.tools/skewer https://sources.debian.org/src/skewer/ https://github.com/relipmoc/skewer |
SCR_001151 | skewer - A fast and sensitive adapter trimmer for illumina paired-end sequences | 2026-02-14 02:05:24 | 11 | |||||
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BAliBASE Resource Report Resource Website 10+ mentions |
BAliBASE (RRID:SCR_001940) | BAliBASE | data or information resource, software resource, source code, data set |
A collection of high quality multiple sequence alignments for objective, comparative studies of alignment algorithms. The alignments are constructed based on 3D structure superposition and manually refined to ensure alignment of important functional residues. A number of subsets are defined covering many of the most important problems encountered when aligning real sets of proteins. It is specifically designed to serve as an evaluation resource to address all the problems encountered when aligning complete sequences. The first release provided sets of reference alignments dealing with the problems of high variability, unequal repartition and large N/C-terminal extensions and internal insertions. Version 2.0 of the database incorporates three new reference sets of alignments containing structural repeats, trans-membrane sequences and circular permutations to evaluate the accuracy of detection/prediction and alignment of these complex sequences. Within the resource, users can look at a list of all the alignments, download the whole database by ftp, get the "c" program to compare a test alignment with the BAliBASE reference (The source code for the program is freely available), or look at the results of a comparison study of several multiple alignment programs, using BAliBASE reference sets. |
benchmark alignment, circular permutation, transmembrane sequence, multiple sequence alignment, benchmark, reference alignment, sequence alignment, sequence, alignment |
is listed by: OMICtools has parent organization: University of Strasbourg; Strasbourg; France |
PMID:16044462 PMID:11125126 PMID:10068696 |
Free, Available for download, Freely available | nif-0000-02594, OMICS_00971 | http://www-bio3d-igbmc.u-strasbg.fr/balibase/, http://www-igbmc.u-strasbg.fr/BioInfo/BAliBASE2/index.html | SCR_001940 | Benchmark Alignment dataBASE | 2026-02-14 02:05:15 | 24 | |||||
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International Gene Trap Consortium Resource Report Resource Website 10+ mentions |
International Gene Trap Consortium (RRID:SCR_002305) | IGTC | biomaterial supply resource, cell repository, material resource | Consortium represents all publicly available gene trap cell lines, which are available on non-collaborative basis for nominal handling fees. Researchers can search and browse IGTC database for cell lines of interest using accession numbers or IDs, keywords, sequence data, tissue expression profiles and biological pathways, can find trapped genes of interest on IGTC website, and order cell lines for generation of mutant mice through blastocyst injection. Consortium members include: BayGenomics (USA), Centre for Modelling Human Disease (Toronto, Canada), Embryonic Stem Cell Database (University of Manitoba, Canada), Exchangeable Gene Trap Clones (Kumamoto University, Japan), German Gene Trap Consortium provider (Germany), Sanger Institute Gene Trap Resource (Cambridge, UK), Soriano Lab Gene Trap Resource (Mount Sinai School of Medicine, New York, USA), Texas Institute for Genomic Medicine - TIGM (USA), TIGEM-IRBM Gene Trap (Naples, Italy). | embryo, embryonic, gene, genome, allele, analysis, assay, bioinformatics, blastocyst, cell, colony, consortium, genotyping, hybridization, in situ, international, knockout, murine, mutant, mutation, probe, qpcr, researcher, scientist, sequence, stem cell, tagging, trap, vector, cell line, embryonic stem cell line, FASEB list |
is listed by: One Mind Biospecimen Bank Listing is related to: Centre for Modeling Human Disease Gene Trap Resource has parent organization: University of California at San Francisco; California; USA is parent organization of: International Gene Trap Consortium Pathways |
NCRR P41 RR01081 | PMID:16381950 | Restricted | nif-0000-00036 | https://igtc.org/ | SCR_002305 | International Gene Trap Consortium | 2026-02-14 02:05:21 | 43 | ||||
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PhyloPythia Resource Report Resource Website |
PhyloPythia (RRID:SCR_000540) | PhyloPythia | data analysis service, production service resource, service resource, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Data analysis service for accurate phylogenetic classification of variable-length DNA fragments. | classification, phyolgenetic, dna fragment, dna, metagenome, sequence | is listed by: OMICtools | PMID:17179938 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01459 | SCR_000540 | 2026-02-14 02:05:32 | 0 | |||||||
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dbSTS Resource Report Resource Website 1+ mentions |
dbSTS (RRID:SCR_000400) | dbSTS | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, as of October 1, 2013; however, the site is still accessible. NCBI resource that contains sequence and mapping data on short genomic landmark sequences or Sequence Tagged Sites. STS sequences are incorporated into the STS Division of GenBank. The dbSTS database offers a route for submission of STS sequences to GenBank. It is designed especially for the submission of large batches of STS sequences. | genomic, mapping, sequence, gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: NCBI |
NIH | PMID:2781285 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:dbsts, nif-0000-20939, r3d100010649 | https://bio.tools/dbsts https://doi.org/10.17616/R39P5C |
SCR_000400 | NCBI dbSTS: database of Sequence Tagged Sites, Sequence Tagged Sites Database, NCBI dbSTS, dbSTS: database of Sequence Tagged Sites, Database of Sequence Tagged Sites | 2026-02-14 02:05:43 | 3 | ||||
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Interolog/Regulog Database Resource Report Resource Website 1+ mentions |
Interolog/Regulog Database (RRID:SCR_000755) | data or information resource, database | Interolog/Regulog quantitatively assess the degree to which interologs can be reliably transferred between species as a function of the sequence similarity of the corresponding interacting proteins. | interacting, interolog, protein, regulog, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Yale University; Connecticut; USA |
PMID:15173116 | nif-0000-20863, biotools:interolog | https://bio.tools/interolog | SCR_000755 | Interolog | 2026-02-14 02:05:33 | 2 | |||||||
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GTEx eQTL Browser Resource Report Resource Website 100+ mentions |
GTEx eQTL Browser (RRID:SCR_001618) | data or information resource, database | Database and browser that provides a central resource to archive and display association between genetic variation and high-throughput molecular-level phenotypes. This effort originated with the NIH GTEx roadmap project: however the scope of this resource will be extended to include any available genotype/molecular phenotype datasets. | genetic variation, high-throughput, phenotype, genotype, molecular, molecule, gene, gene expression, snp, trait, expression, quantitative trait locus, expression quantitative trait locus, genome, probe, sequence, statistics, p-value, rna-seq, array, lymphoblastoid, liver, cerebellum, frontal cortex, temporal cortex, pons, gene regulation, tissue, mrna, data set | has parent organization: NCBI | NIH Common Fund 268201000029C-4-0-2 | Free, Freely available | nlx_153884 | http://www.gtexportal.org/home/ | SCR_001618 | NCBI GTEx eQTL Browser, Genotype-Tissue Expression eQTL Browser, GTEx (Genotype-Tissue Expression) eQTL Browser, NCBI GTeX eQTL Browser | 2026-02-14 02:06:02 | 111 | ||||||
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Neurospora crassa Database Resource Report Resource Website 1+ mentions |
Neurospora crassa Database (RRID:SCR_001372) | NCD | data or information resource, database | It's strategy involves Whole Genome Shotgun (WGS) sequencing, in which sequence from the entire genome is generated and reassembled. This method is standard for microbial genome sequencing, and has been successfully applied to Drosophila. Neurospora is an ideal candidate for this approach because of the low repeat content of the genome. Neurospora crassa Database has expanded the scope of its database by including a mitochondrial annotation, incorporating information from the Neurospora compendium, and assigning NCU numbers to tRNA and rRNAs. They have improved the annotation process to predict untranslated regions and to reduce the number of spurious predictions. As a result, version 3 contains 9,826 genes, 794 fewer than version 2. During the initial phase of a WGS project they sequence both ends of the 4 kb inserts from a plasmid library prepared using randomly sheared and sized-selected DNA. The shotgun reads are assembled by recognizing overlapping regions of sequence and making use of the knowledge of the orientation and distance of the paired reads from each plasmid. Obtaining deep sequence coverage though high levels of sequence redundancy assures that the majority of the genome is represented in the initial assembly and that the consensus sequence is of high quality. Their approach toward the initial assembly was conservative, meaning they would rather fail to join sequence contigs that might overlap each other than risk making false joins between two closely related but non-overlapping genomic regions. Hence, the initial assembly contains many sequence contigs and over time these contigs will increase in size and decrease in number as they are joined together. After shotgun sequencing and assembly there was a second phase of sequencing in which additional sequence was obtained from specific regions that were missing from the original assembly or are recognized to be of low quality in the consensus. The Neurospora crassa sequencing project reflects a close collaboration between the Broad Institute and the Neurospora research community. Principal investigators include Bruce Birren and Chad Nusbaum from the Broad Institute, Matt Sachs at the Oregon Graduate Institute of Science and Technology, Chuck Staben at the University of Kentucky and Jak Kinsey at the Fungal Genetics Stock Center at the University of Kansas Medical Center. In addition, we have a larger Advisory Board made up of a number of Neurospora researchers. Sponsors: They have been funded by the National Science Foundation to sequence the N. crassa genome and make the information publicly available. | gene, annotation, compendium, contig, distance, drosophila, genome, mitochondrial, neurospora crassa, plasmid, region, rrna, sequence, trna, untranslated | Free, Freely available, | nif-0000-20965 | http://www.broadinstitute.org/annotation/genome/neurospora/Home.html | SCR_001372 | Neurospora crassa Database | 2026-02-14 02:06:01 | 4 | |||||||
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LSPD Resource Report Resource Website 1+ mentions |
LSPD (RRID:SCR_002125) | LSPD | data or information resource, database | LSPD provides liver specific gene. It lists ~300 promoter regions responsible for liver specific transcriptions, collect ~400 experimentally verified regulatory regions and elements, provide information on transcription regulation of liver genes, compare transcription regulation of functionally or evolutionarily related genes, and retrieve sequences of the promoter region. Its regulatory elements provides information on transcription regulatory elements, reports the methods for verification of the elements, records binding affinity and regulatory function, and summarizes the site distribution and sequence consensus. | liver gene, promoter region, regulatory region, sequence, transcription | Free, Freely Available | nif-0000-20920 | SCR_002125 | The Liver Specific Gene Promoter Database | 2026-02-14 02:05:38 | 6 | ||||||||
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Conserved Domain Database Resource Report Resource Website 100+ mentions |
Conserved Domain Database (RRID:SCR_002077) | CDD | data or information resource, database | Database of annotations of functional units in proteins including multiple sequence alignment models for ancient domains and full-length proteins. This collection of models includes 3D structures that display the sequence/structure/function relationships in proteins. It also includes alignments of the domains to known three-dimensional protein structures in the MMDB database. The source databases are Pfam, Smart, and COG. Users can identify amino acids in protein sequences with the resources available as well as view single sequences embedded within multiple sequence alignments. | protein, amino acid sequence, nucleic acid, 3d structure, annotation, function, sequence, structure, amino acid, gold standard |
is used by: Mutation Annotation and Genomic Interpretation is listed by: re3data.org is related to: Pfam is related to: SMART is related to: COG is related to: NCBI Structure has parent organization: NCBI works with: Conserved Domains Search |
PMID:25414356 PMID:18984618 |
nif-0000-02647 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd | SCR_002077 | Conserved Domains Database, Conserved Domains | 2026-02-14 02:05:46 | 306 | ||||||
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UniProt Resource Report Resource Website 10000+ mentions |
UniProt (RRID:SCR_002380) | UniProt | data or information resource, database | Collection of data of protein sequence and functional information. Resource for protein sequence and annotation data. Consortium for preservation of the UniProt databases: UniProt Knowledgebase (UniProtKB), UniProt Reference Clusters (UniRef), and UniProt Archive (UniParc), UniProt Proteomes. Collaboration between European Bioinformatics Institute (EMBL-EBI), SIB Swiss Institute of Bioinformatics and Protein Information Resource. Swiss-Prot is a curated subset of UniProtKB. | collection, protein, sequence, annotation, data, functional, information |
is used by: LIPID MAPS Proteome Database is used by: ChannelPedia is used by: Open PHACTS is used by: DisGeNET is used by: Smart Dictionary Lookup is used by: MitoMiner is used by: Cytokine Registry is used by: MobiDB is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: Phospho.ELM is used by: GEROprotectors is used by: SwissLipids is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: LabWorm is related to: Clustal W2 is related to: UniProt DAS is related to: UniParc at the EBI is related to: ProDom is related to: LegumeIP is related to: Pathway Commons is related to: NIH Data Sharing Repositories is related to: FlyMine is related to: IMEx - The International Molecular Exchange Consortium is related to: 3D-Interologs is related to: Biomine is related to: EBIMed is related to: STOP is related to: Coremine Medical is related to: BioExtract is related to: STRAP is related to: GOTaxExplorer is related to: GoAnnotator is related to: IT-GOM: Integrated Tool for IC-based GO Semantic Similarity Measures is related to: Whatizit is related to: MOPED - Model Organism Protein Expression Database is related to: Polbase is related to: PredictSNP is related to: PSICQUIC Registry is related to: IntAct is related to: p300db is related to: UniProt Proteomes is related to: SARS-CoV-2 mutation effects and 3D structure prediction from sequence covariation has parent organization: European Bioinformatics Institute has parent organization: SIB Swiss Institute of Bioinformatics has parent organization: Protein Information Resource is parent organization of: UniProtKB is parent organization of: NEWT is parent organization of: UniParc is parent organization of: UniProt Chordata protein annotation program is parent organization of: UniRef works with: Genotate works with: CellPhoneDB works with: MOLEonline works with: MiMeDB |
NHGRI U41 HG006104; NHGRI P41 HG02273; NIGMS 5R01GM080646; NIGMS R01 GM080646; NLM G08 LM010720; NCRR P20 RR016472; NSF DBI-0850319; British Heart Foundation ; NEI ; NHLBI ; NIA ; NIAID ; NIDDK ; NIMH ; NCI ; EMBL ; PDUK ; ARUK ; NHGRI U24 HG007722 |
PMID:19843607 PMID:18836194 PMID:18045787 PMID:17142230 PMID:16381842 PMID:15608167 PMID:14681372 |
nif-0000-00377, SCR_018750, r3d100010357 | http://www.ebi.uniprot.org http://www.uniprot.org/uniprot/ http://www.pir.uniprot.org ftp://ftp.uniprot.org https://doi.org/10.17616/R3BW2M |
SCR_002380 | , The Universal Protein Resource, Universal Protein Resource, UNIPROT Universal Protein Resource | 2026-02-14 02:05:47 | 17565 | |||||
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Human Proteomics Initiative Resource Report Resource Website |
Human Proteomics Initiative (RRID:SCR_002373) | HPI | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 03, 2011. IT HAS BEEN REPLACED BY A NEW UniProtKB/Swiss-Prot ANNOTATION PROGRAM CALLED UniProt Chordata protein annotation program. The Human Proteome Initiative (HPI) aims to annotate all known human protein sequences, as well as their orthologous sequences in other mammals, according to the quality standards of UniProtKB/Swiss-Prot. In addition to accurate sequences, we strive to provide, for each protein, a wealth of information that includes the description of its function, domain structure, subcellular location, similarities to other proteins, etc. Although as complete as currently possible, the human protein set they provide is still imperfect, it will have to be reviewed and updated with future research results. They will also create entries for newly discovered human proteins, increase the number of splice variants, explore the full range of post-translational modifications (PTMs) and continue to build a comprehensive view of protein variation in the human population. The availability of the human genome sequence has enabled the exploration and exploitation of the human genome and proteome to begin. Research has now focused on the annotation of the genome and in particular of the proteome. With expert annotation extracted from the literature by biologists as the foundation, it has been possible to expand into the areas of data mining and automatic annotation. With further development and integration of pattern recognition methods and the application of alignments clustering, proteome analysis can now be provided in a meaningful way. These various approaches have been integrated to attach, extract and combine as much relevant information as possible to the proteome. This resource should be valuable to users from both research and industry. We maintain a file containing all human UniProtKB/Swiss-Prot entries. This file is updated at every biweekly release of UniProt and can be downloaded by FTP download, HTTP download or by using a mirroring program which automatically retrieves the file at regular intervals. | function, gene, alignment, biologist, clustering, coding, development, genome, human, location, mammalian, modification, ortholog, population, post-translational, protein, proteome, proteomic, proteomics, sequence, splice, structure, subcellular, variant, variation, gold standard |
is related to: UniProt Chordata protein annotation program has parent organization: SIB Swiss Institute of Bioinformatics |
PMID:11301130 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21199 | SCR_002373 | Human Proteome Initiative, UniProtKB/Swiss-Prot Human Proteome Initiative | 2026-02-14 02:05:47 | 0 | ||||||
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AceView Resource Report Resource Website 100+ mentions |
AceView (RRID:SCR_002277) | AceView/WormGenes | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented August 29, 2016. AceView offers an integrated view of the human, nematode and Arabidopsis genes reconstructed by co-alignment of all publicly available mRNAs and ESTs on the genome sequence. Our goals are to offer a reliable up-to-date resource on the genes and their functions and to stimulate further validating experiments at the bench. AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-aligned on the genome then clustered into a minimal number of alternative transcript variants and grouped into genes. Using exhaustively and with high quality standards the available cDNA sequences evidences the beauty and complexity of mammals' transcriptome, and the relative simplicity of the nematode and plant transcriptomes. Genes are classified according to their inferred coding potential; many presumably non-coding genes are discovered. Genes are named by Entrez Gene names when available, else by AceView gene names, stable from release to release. Alternative features (promoters, introns and exons, polyadenylation signals) and coding potential, including motifs, domains, and homologies are annotated in depth; tissues where expression has been observed are listed in order of representation; diseases, phenotypes, pathways, functions, localization or interactions are annotated by mining selected sources, in particular PubMed, GAD and Entrez Gene, and also by performing manual annotation, especially in the worm. In this way, both the anatomy and physiology of the experimentally cDNA supported human, mouse and nematode genes are thoroughly annotated. Our goals are to offer an up-to-date resource on the genes, in the hope to stimulate further experiments at the bench, or to help medical research. AceView can be queried by meaningful words or groups of words as well as by most standard identifiers, such as gene names, Entrez Gene ID, UniGene ID, GenBank accessions. | est, exon, expression, function, gene, alignment, arabidopsis, cdna, co-alignment, coding, disease, genome, genomic, human, intron, localization, mammal, mouse, mrna, nematode, pathway, phenotype, plant, polyadenylation, promoter, rat, sequence, signal, tissue, transcript, transcriptome, worm, blast, gold standard | has parent organization: NCBI | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21007, r3d100010651 | https://doi.org/10.17616/R3260G | http://www.ncbi.nih.gov/IEB/Research/Acembly/ | SCR_002277 | AceView genes, AceView/WormGenes, The AceView Genes | 2026-02-14 02:05:39 | 186 | |||||
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Full-Malaria: Malaria Full-Length cDNA Database Resource Report Resource Website 1+ mentions |
Full-Malaria: Malaria Full-Length cDNA Database (RRID:SCR_002348) | data or information resource, database | FULL-malaria is a database for a full-length-enriched cDNA library from the human malaria parasite Plasmodium falciparum. Because of its medical importance, this organism is the first target for genome sequencing of a eukaryotic pathogen; the sequences of two of its 14 chromosomes have already been determined. However, for the full exploitation of this rapidly accumulating information, correct identification of the genes and study of their expression are essential. Using the oligo-capping method, this database has produced a full-length-enriched cDNA library from erythrocytic stage parasites and performed one-pass reading. The database consists of nucleotide sequences of 2490 random clones that include 390 (16%) known malaria genes according to BLASTN analysis of the nr-nt database in GenBank; these represent 98 genes, and the clones for 48 of these genes contain the complete protein-coding sequence (49%). On the other hand, comparisons with the complete chromosome 2 sequence revealed that 35 of 210 predicted genes are expressed, and in addition led to detection of three new gene candidates that were not previously known. In total, 19 of these 38 clones (50%) were full-length. From these observations, it is expected that the database contains approximately 1000 genes, including 500 full-length clones. It should be an invaluable resource for the development of vaccines and novel drugs. Full-malaria has been updated in at least three points. (i) 8934 sequences generated from the addition of new libraries added so that the database collection of 11,424 full-length cDNAs covers 1375 (25%) of the estimated number of the entire 5409 parasite genes. (ii) All of its full-length cDNAs and GenBank EST sequences were mapped to genomic sequences together with publicly available annotated genes and other predictions. This precisely determined the gene structures and positions of the transcriptional start sites, which are indispensable for the identification of the promoter regions. (iii) A total of 4257 cDNA sequences were newly generated from murine malaria parasites, Plasmodium yoelii yoelii. The genome/cDNA sequences were compared at both nucleotide and amino acid levels, with those of P.falciparum, and the sequence alignment for each gene is presented graphically. This part of the database serves as a versatile platform to elucidate the function(s) of malaria genes by a comparative genomic approach. It should also be noted that all of the cDNAs represented in this database are supported by physical cDNA clones, which are publicly and freely available, and should serve as indispensable resources to explore functional analyses of malaria genomes. Sponsors: This database has been constructed and maintained by a Grant-in-Aid for Publication of Scientific Research Results from the Japan Society for the Promotion of Science (JSPS). This work was also supported by a Special Coordination Funds for Promoting Science and Technology from the Science and Technology Agency of Japan (STA) and a Grant-in-Aid for Scientific Research on Priority Areas from the Ministry of Education, Science, Sports and Culture of Japan. | drug, eukaryotic, expression, function, gene, alignment, amino acid, cdna, chromosome, clone, coding, comparative, genome, genomic, human, malaria, medical, nucleotide, oligo-capping, organism, parasite, pathogen, physical, plasmodium falciparum, promoter, protein, region, sequence, sequencing, unicellular eukaryote genome databases, vaccine | has parent organization: University of Tokyo; Tokyo; Japan | PMID:18987005 PMID:14681428 |
nif-0000-21157 | SCR_002348 | Full-Malaria | 2026-02-14 02:05:47 | 2 | ||||||||
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SECISearch3 and Seblastian Resource Report Resource Website 1+ mentions |
SECISearch3 and Seblastian (RRID:SCR_003186) | SECISearch, Seblastian, SECISearch3 | data analysis service, production service resource, service resource, analysis service resource | Web server to predict eukaryotic selenoproteins and SECIS (SElenoCysteine Insertion Sequences) elements along nucleotide sequences. SECISearch3 replaces its predecessor SECISearch as a tool for prediction of eukaryotic SECIS elements. Seblastian is a method for selenoprotein gene detection that uses SECISearch3 and then predicts selenoprotein sequences encoded upstream of SECIS elements. Seblastian is able to both identify known selenoproteins and predict new selenoproteins. | selenoprotein, nucleotide sequence, selenocysteine insertion sequence, sequence |
is listed by: OMICtools has parent organization: Center for Genomic Regulation; Barcelona; Spain |
PMID:23783574 | Public, Acknowledgement requested | OMICS_01566 | SCR_003186 | Selenoprotein prediction server | 2026-02-14 02:05:43 | 1 | ||||||
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Nucleic Acid Database Resource Report Resource Website 10+ mentions |
Nucleic Acid Database (RRID:SCR_003255) | NDB | data or information resource, database | A database of three-dimensional structural information about nucleic acids and their complexes. In addition to primary data, it contains derived geometric data, classifications of structures and motifs, standards for describing nucleic acid features, as well as tools and software for the analysis of nucleic acids. A variety of search capabilities are available, as are many different types of reports. NDB maintains the macromolecular Crystallographic Information File (mmCIF). | nucleic acid, dna, nucleopeptide, nucleoprotein, nucleotide, rna, transfection, sequence, structure, function, bio.tools, FASEB list |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: MINAS - Metal Ions in Nucleic AcidS is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: Jenalib: Jena Library of Biological Macromolecules has parent organization: Rutgers University; New Jersey; USA |
NSF ; DOE ; NIH |
PMID:24185695 PMID:1384741 |
Free, Available for download, Freely available | nif-0000-03184, biotools:ndb, r3d100010415 | https://bio.tools/ndb https://doi.org/10.17616/R3531R |
SCR_003255 | 2026-02-14 02:05:49 | 36 | |||||
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NCBI Taxonomy Resource Report Resource Website 100+ mentions |
NCBI Taxonomy (RRID:SCR_003256) | NCBI Taxonomy | data or information resource, database | Database for a curated classification and nomenclature that contains the names of all organisms that are represented in the public sequence databases with at least one nucleotide or protein sequence. Data provided encompasses archaea, bacteria, eukaryota, viroids and viruses. The NCBI taxonomy database is not a primary source for taxonomic or phylogenetic information. Furthermore, the database does not follow a single taxonomic treatise but rather attempts to incorporate phylogenetic and taxonomic knowledge from a variety of sources, including the published literature, web-based databases, and the advice of sequence submitters and outside taxonomy experts. Consequently, the NCBI taxonomy database is not a phylogenetic or taxonomic authority and should not be cited as such. | viroid, virus, nucleotide, protein, sequence, phylogeny, taxonomic, taxonomy, nomenclature, cladistics, classification, animal, genetic code, gold standard |
is used by: NIF Data Federation is used by: Vertebrate Taxonomy Ontology is listed by: re3data.org is related to: Taxonomy is related to: NEWT is related to: Phenoscape Knowledgebase is related to: EBIMed is related to: GOTaxExplorer is related to: Whatizit is related to: Integrated Manually Extracted Annotation has parent organization: NCBI is parent organization of: NCBITaxon |
PMID:18940862 PMID:18940867 |
Free, Freely available | nif-0000-03179, r3d100010776 | http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html https://doi.org/10.17616/R3X039 |
SCR_003256 | NCBI Taxonomy Browser, Taxonomy Browser, Entrez Taxonomy Browser, NCBI Taxonomy Database | 2026-02-14 02:06:14 | 273 | |||||
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mtDB - Human Mitochondrial Genome Database Resource Report Resource Website 50+ mentions |
mtDB - Human Mitochondrial Genome Database (RRID:SCR_002945) | mtDB | data or information resource, database | A database of human mitochondrial genomes containing mtDNA sequences, polymorphic sites, and the ability to search for specific variants. It contains 1865 complete sequences and 839 coding region sequences. | human genome, mitochondrial dna, sequence, variant, population genetics, coding region, polymorphic site, population, mitochondrial sequence, mitochondrial polymorphism, FASEB list |
is listed by: OMICtools has parent organization: Uppsala University; Uppsala; Sweden |
Swedish Research Council | PMID:16381973 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02994, OMICS_01642 | SCR_002945 | Human Mitochondrial Genome Database | 2026-02-14 02:06:09 | 58 | |||||
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ASAP: the Alternative Splicing Annotation Project Resource Report Resource Website 10+ mentions |
ASAP: the Alternative Splicing Annotation Project (RRID:SCR_003415) | ASAP | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on 8/12/13. Database to access and mine alternative splicing information coming from genomics and proteomics based on genome-wide analyses of alternative splicing in human (30 793 alternative splice relationships found) from detailed alignment of expressed sequences onto the genomic sequence. ASAP provides precise gene exon-intron structure, alternative splicing, tissue specificity of alternative splice forms, and protein isoform sequences resulting from alternative splicing. They developed an automated method for discovering human tissue-specific regulation of alternative splicing through a genome-wide analysis of expressed sequence tags (ESTs), which involves classifying human EST libraries according to tissue categories and Bayesian statistical analysis. They use the UniGene clusters of human Expressed Sequence Tags (ESTs) to identify splices. The UniGene EST's are clustered so that a single cluster roughly corresponds to a gene (or at least a part of a gene). A single EST represents a portion of a processed (already spliced) mRNA. A given cluster contains many ESTs, each representing an outcome of a series of splicing events. The ESTs in UniGene contain the different mRNA isoforms transcribed from an alternatively spliced gene. They are not predicting alternative splicing, but locating it based on EST analysis. The discovered splices are further analyzed to determine alternative splicing events. They have identified 6201 alternative splice relationships in human genes, through a genome-wide analysis of expressed sequence tags (ESTs). Starting with 2.1 million human mRNA and EST sequences, they mapped expressed sequences onto the draft human genome sequence and only accepted splices that obeyed the standard splice site consensus. After constructing a tissue list of 46 human tissues with 2 million human ESTs, they generated a database of novel human alternative splices that is four times larger than our previous report, and used Bayesian statistics to compare the relative abundance of every pair of alternative splices in these tissues. Using several statistical criteria for tissue specificity, they have identified 667 tissue-specific alternative splicing relationships and analyzed their distribution in human tissues. They have validated our results by comparison with independent studies. This genome-wide analysis of tissue specificity of alternative splicing will provide a useful resource to study the tissue-specific functions of transcripts and the association of tissue-specific variants with human diseases. | gene, genome, human, isoform, mechanism, metazoa, molecular, mrna, nucleus, process, protein, sequence, splice, tissue specificity, transcription, transcript, alternate splicing, microarray, alternative splicing, biological process, alternatively spliced isoform, contig, cancer, image |
is listed by: Biositemaps is related to: Alternative Splicing Annotation Project II Database has parent organization: University of California at Los Angeles; California; USA |
NSF 0082964; NSF DGE-9987641; DOE DEFG0387ER60615 |
PMID:12519958 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33105 | SCR_003415 | Alternative Splicing, Alternative Splicing Annotation Project, Alternative Splicing Annotation Project database | 2026-02-14 02:05:49 | 33 | |||||
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MITOMAP - A human mitochondrial genome database Resource Report Resource Website 100+ mentions |
MITOMAP - A human mitochondrial genome database (RRID:SCR_002996) | MITOMAP | data or information resource, database | Database of polymorphisms and mutations of the human mitochondrial DNA. It reports published and unpublished data on human mitochondrial DNA variation. All data is curated by hand. If you would like to submit published articles to be included in mitomap, please send them the citation and a pdf. | gene, genome, diabetes, disease, disease-association, high resolution screening, human, inversion, metabolism, mitochondrial dna, mutation, phenotype, polymorphism, polypeptide assignment, pseudogene, restriction site, rna, sequence, trna, unpublished, variation, mitochondria, dna, insertion, deletion, FASEB list |
is used by: HmtVar is listed by: OMICtools is related to: Hereditary Hearing Loss Homepage has parent organization: Childrens Hospital of Philadelphia - Research Institute; Pennsylvania; USA has parent organization: Emory University School of Medicine; Atlanta; Georgia; USA |
NIH ; Muscular Dystrophy Foundation ; Ellison Foundation ; Diputacion General de Aragon Grupos consolidados B33 ; NIGMS GM46915; NINDS NS21328; NHLBI HL30164; NIA AG10130; NIA AG13154; NINDS NS213L8; NHLBI HL64017; NIH Biomedical Informatics Training Grant T15 LM007443; NSF EIA-0321390; Spanish Fondo de Investigacion Sanitaria PI050647; Ciber Enfermedades raras CB06/07/0043 |
PMID:17178747 PMID:15608272 PMID:9399813 PMID:9016535 PMID:8594574 |
Except where otherwise noted, Creative Commons Attribution License, The community can contribute to this resource | nif-0000-00511, OMICS_01641 | SCR_002996 | 2026-02-14 02:05:42 | 368 |
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