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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
HapCompass
 
Resource Report
Resource Website
1+ mentions
HapCompass (RRID:SCR_000942) algorithm Software that utilizes a fast cycle basis algorithm for the accurate haplotype assembly of sequence data. It is able to create pairwise SNP phasings. algorithm, haplotype, sequence, genome, dna, rna, snp is listed by: OMICtools
has parent organization: Brown University; Rhode Island; USA
NSF 1048831;
NSF 1321000
THIS RESOURCE IS NO LONGER IN SERVICE OMICS_00197 SCR_000942 2026-09-05 06:24:27 1
R453Plus1Toolbox
 
Resource Report
Resource Website
1+ mentions
R453Plus1Toolbox (RRID:SCR_001105) data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit R software toolbox of functions for the analysis of data generated by Roche's 454 sequencing platform. Additional functions are included for quality assurance, annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. A pipeline for the detection of structural variants is provided. genome, sequence, visualization, structural variants, r, sequence analysis software is listed by: OMICtools
is hosted by: Bioconductor
PMID:21349869 Free, Available for download, Freely available OMICS_01354 SCR_001105 2026-09-05 06:24:29 4
BreakFusion
 
Resource Report
Resource Website
1+ mentions
BreakFusion (RRID:SCR_001102) BreakFusion software resource Software package written in Perl and C++ that provides a computational pipeline for identifying gene fusions from RNA-seq data. computational pipeline, gene fusions, rna, sequence, data, perl, c++ is listed by: OMICtools
has parent organization: University of Texas MD Anderson Cancer Center
PMID:22563071
DOI:10.1093/bioinformatics/bts272
Free, Available for download, Freely available OMICS_01342 SCR_001102 2026-09-05 06:24:29 3
Kyoto Encyclopedia of Genes and Genomes Expression Database
 
Resource Report
Resource Website
1000+ mentions
Kyoto Encyclopedia of Genes and Genomes Expression Database (RRID:SCR_001120) KEGG Expression Database data or information resource, data repository, database, service resource, storage service resource Database for mapping gene expression profiles to pathways and genomes. Repository of microarray gene expression profile data for Synechocystis PCC6803 (syn), Bacillus subtilis (bsu), Escherichia coli W3110 (ecj), Anabaena PCC7120 (ana), and other species contributed by the Japanese research community. encyclopedia, endogenous, environment, enzyme, escherichia coli, exogenous, expression, family, functional, gene, genetic, anabaena, bacillus subtilis, biological system, biology, building block, cell, cellular, chemical, community, complex, genome, genomic, hierarchy, interaction, japanese, mapping, metabolic, metabolic pathway databases, microarray, molecular, molecular wiring, nomenclature, order, organism, ortholog, pathway, process, protein, reaction, research, sequence, specie, substance, synechocystis, FASEB list is listed by: LabWorm
is affiliated with: KEGG
has parent organization: Kyoto University; Kyoto; Japan
PMID:9847135
PMID:10592173
Free, Available for download, Freely available r3d100011570, nif-0000-21234 https://doi.org/10.17616/R3792T SCR_001120 Kyoto Encyclopedia of Genes and Genomes Expression Database 2026-09-05 06:24:29 1279
Reaper - Demultiplexing trimming and filtering sequencing data
 
Resource Report
Resource Website
1+ mentions
Reaper - Demultiplexing trimming and filtering sequencing data (RRID:SCR_001144) Reaper software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. Software program for demultiplexing, trimming and filtering short read sequencing data. c, alignment, sequence, demultiplex, trim, filter, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: European Bioinformatics Institute
THIS RESOURCE IS NO LONGER IN SERVICE biotools:reaper, OMICS_02157 https://bio.tools/reaper SCR_001144 2026-09-05 06:24:30 1
Genome Trax
 
Resource Report
Resource Website
1+ mentions
Genome Trax (RRID:SCR_001234) Genome Trax service resource Service that provides a comprehensive compilation of variant knowledge that allows you to identify pathogenic variants in human whole genome or exome sequences. It makes it easy to upload a complete genome?s worth of variations and identify the biologically relevant subset of known mutations, mutations that are novel and appear in a candidate disease genes, or mutations that are predicted to have a deleterious effect. The database includes a comprehensive collection of disease causing mutations from HGMD Professional, regulatory sites from TRANSFAC , and disease genes, drug targets and pathways from PROTEOME, as well as pharmacogenomic variants. It integrates the best public data-sets on somatic mutations, allele frequencies and clinical variants, in their most up-to-date version, for a total of more than 165 million annotations. It is possible to identify known pathogenic variants, remove harmless common variants, and obtain deleterious predictions for novel variants. With family data, it is possible to identify variants that are de novo, compound heterozygous only in the offspring. All of the results can be downloaded to Excel for further review. For core facilities and bioinformaticians, the complete underlying data is made available for download and easy integration into custom analysis pipelines. Genome Trax data is optimized to work with many other software packages, such as ANNOVARTM, CLC bio, Alamut, SimulConsult, and Cartagenia. next-generation sequencing, genome, exome, sequence, variation, mutation, pathogenic, database, bio.tools, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: BIOBASE Corporation
THIS RESOURCE IS NO LONGER IN SERVICE OMICS_02109, biotools:genome_trax https://bio.tools/genome_trax SCR_001234 Genome Trax for Next Generation Sequencing 2026-09-05 06:24:31 2
TALLYMER
 
Resource Report
Resource Website
1+ mentions
TALLYMER (RRID:SCR_001244) Tallymer software resource A collection of flexible and memory-efficient software programs for k-mer counting and indexing of large sequence sets. It is based on enhanced suffix arrays which gives a much larger flexibility concerning the choice of the k-mer size. It can process large data sizes of several billion bases. k-mer, counting, sequence, genome annotation, genome, annotation, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: University of Hamburg; Hamburg; Germany
PMID:18976482 Free, Freely available biotools:tallymer, OMICS_02096 https://bio.tools/tallymer SCR_001244 2026-09-05 06:24:31 7
Morpholino Database
 
Resource Report
Resource Website
1+ mentions
Morpholino Database (RRID:SCR_001378) MODB data or information resource, data repository, database, service resource, storage service resource Central database to house data on morpholino screens currently containing over 700 morpholinos including control and multiple morpholinos against the same target. A publicly accessible sequence-based search opens this database for morpholinos against a particular target for the zebrafish community. Morpholino Screens: They set out to identify all cotranslationally translocated genes in the zebrafish genome (Secretome/CTT-ome). Morpholinos were designed against putative secreted/CTT targets and injected into 1-4 cell stage zebrafish embryos. The embryos were observed over a 5 day period for defects in several different systems. The first screen examined 184 gene targets of which 26 demonstrated defects of interest (Pickart et al. 2006). A collaboration with the Verfaillie laboratory examined the knockdown of targets identified in a comparative microarray analysis of hematopoietic stem cells demonstrating how microarray and morpholino technologies can be used in conjunction to enrich for defects in specific developmental processes. Currently, many collaborations are underway to identify genes involved in morphological, kidney, skin, eye, pigment, vascular and hematopoietic development, lipid metabolism and more. The screen types referred to in the search functions are the specific areas of development that were examined during the various screens, which include behavior, general morphology, pigmentation, toxicity, Pax2 expression, and development of the craniofacial structures, eyes, kidneys, pituitary, and skin. Only data pertaining to specific tests performed are presented. Due to the complexity of this international collaboration and time constraints, not all morpholinos were subjected to all screen types. They are currently expanding public access to the database. In the future we will provide: * Mortality curves and dose range for each morpholino * Preliminary data regarding the effectiveness of each morpholino * Expanded annotation for each morpholino * External linkage of our morpholino sequences to ZFIN and Ensembl. To submit morpholino-knockdown results to MODB please contact the administrator for a user name and password. morpholino, target mrna, embryonic zebrafish, sequence, target, blast, phenotype, anatomy, development, behavior, morphology, pigmentation, toxicity, pax2 expression, craniofacial structure, eye, kidney, pituitary, skin, name, target name, target sequence, gene target, genetic, mortality, toxicity, defect, function, gene annotation, genome, data analysis service uses: Zebrafish Information Network (ZFIN)
uses: PATO
has parent organization: Mayo Clinic Minnesota; Minnesota; USA
NIGMS GM63904;
NIA CA65493
PMID:18179718 THIS RESOURCE IS NO LONGER IN SERVICE nlx_152566 SCR_001378 MODB (MOprholino DataBase) 2026-09-05 06:24:34 1
Integrated DNA Technologies OligoAnalyzer
 
Resource Report
Resource Website
500+ mentions
Integrated DNA Technologies OligoAnalyzer (RRID:SCR_001363) OligoAnalyzer data analysis software, data processing software, sequence analysis software, software application, software resource, web application Web-based application for analyzing oligonucleotides. Analysis proceeds after the sequence has been entered and the calculations modified based on target type, oligo concentration, sodium ion concentration, magnesium ion concentration, and dNTP concentration. oligos, oligonucleotides, sequence, web, analyzer Free, Freely Available nif-0000-07754 SCR_001363 IDT OligoAnalyzer, OligoAnalyzer, IDT Oligo Analyzer, OligoAnalyzer 3.1 2026-09-05 06:24:33 620
GlySeq
 
Resource Report
Resource Website
1+ mentions
GlySeq (RRID:SCR_001569) GlySeq analysis service resource, data analysis service, data or information resource, data set, production service resource, service resource Service dedicated to statistically analyze the sequences around glycosylation sites. Glycosylation belongs to the most common and most important co- and postranslational modifications of proteins. Since it is often difficult to determine which potential glycosylation sites are in fact glycosylated, there is only few data available about glycoproteins. Sources from which such data can be retrieved are SwissProt and the Protein Data Bank (PDB). Data from the PDB is obtained using pdb2linucs and updated weekly. GlySeq is dedicated to statistically analyze these sequences, especially the areas around glycosylation sites. sequence, glycosylation site, glycoprotein sequence, glycoprotein, carbohydrate is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB)
is related to: pdb2linucs
has parent organization: glycosciences.de
DFG PMID:15608187 THIS RESOURCE IS NO LONGER IN SERVICE nlx_152882 SCR_001569 GlySeq - Statistical Analysis of Glycoprotein Sequences 2026-09-05 06:24:36 1
BLASTN
 
Resource Report
Resource Website
10000+ mentions
BLASTN (RRID:SCR_001598) BLASTn analysis service resource, data analysis service, data or information resource, database, production service resource, service resource Web application to search nucleotide databases using a nucleotide query. Algorithms: blastn, megablast, discontiguous megablast. nucleotide, alignment, compare, sequence, genome, blast, transcript, dna sequence is listed by: OMICtools
is listed by: SoftCite
has parent organization: NCBI
works with: Seek and Blastn
works with: RMBlast
PMID:17666756
PMID:18567917
Free, Freely available nlx_153932, OMICS_00990 http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome SCR_001598 NCBI BLASTN, Nucleotide Blast, Standard Nucleotide BLAST 2026-09-05 06:24:36 21160
Sea Urchin Genome Project
 
Resource Report
Resource Website
1+ mentions
Sea Urchin Genome Project (RRID:SCR_001735) data or information resource, portal, project portal Provides informationa about Genome of California Purple Sea Urchin, one species (Strongylocentrotus purpuratus) of which has been sequenced and annotated by Sea Urchin Genome Sequencing Consortium led by HGSC. Reports sequence and analysis of genome of sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. echinoderm, evolutionary, fragile urchin, gene, genome, allocentrotus fragilis, bacterial artificial chromosome (bac), biology, chromosome, clone, core facility, deuterostome, developmental biology, heterozygosity, metabase, model, sea urchin, sequence, shotgun, strongylocentrotus franciscanus, strongylocentrotus purpuratus, systems biology, vertebrate has parent organization: Baylor University; Texas; USA Free, Freely Available nif-0000-25606, SCR_002841, nif-0000-10253 http://www.hgsc.bcm.tmc.edu/project-species-o-Strongylocentrotus%20purpuratus.hgsc?pageLocation=Strongylocentrotus%20purpuratus SCR_001735 Sea Urchin, HGSC Sea Urchin Genome Project 2026-09-05 06:24:38 1
An Integrated Multiple Structure Visualization and Multiple Sequence Alignment Application
 
Resource Report
Resource Website
An Integrated Multiple Structure Visualization and Multiple Sequence Alignment Application (RRID:SCR_001646) data analysis software, data processing software, data visualization software, rendering software, software application, software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Friend is a bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA. The application provides basic functionalities such as: structure visualization with different rendering and coloring, sequence alignment, and simple phylogeny analysis, along with a number of extended features to perform more complex analyses of sequence structure relationships, including: structural alignment of proteins, investigation of specific interaction motifs, studies of protein-protein and protein-DNA interactions, and protein super-families. Friend is also useful for the functional annotation of proteins, protein modeling, and protein folding studies. Friend provides three levels of usage; 1) an extensive GUI for a scientist with no programming experience, 2) a command line interface for scripting for a scientist with some programming experience, and 3) the ability to extend Friend with user written libraries for an experienced programmer. The application is linked and communicates with local and remote sequence and structure databases. alignment, analysis, bioinformatics, database, dna, interaction, motif, phylogeny, protein, rna, scientist, sequence, structure, super-family, visualization, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: Northeastern University; Massachusetts; USA
PMID:16076889 THIS RESOURCE IS NO LONGER IN SERVICE biotools:friend, nif-0000-10149 https://bio.tools/friend SCR_001646 FRIEND 2026-09-05 06:24:37 0
Prediction of Amyloid Structure Aggregation
 
Resource Report
Resource Website
100+ mentions
Prediction of Amyloid Structure Aggregation (RRID:SCR_001768) PASTA analysis service resource, data analysis service, production service resource, service resource, software resource, web application Online interface that utilizes an algorithm to predict the most aggregation-prone portions and the corresponding beta-strand inter-molecular pairing for a given input sequence. Users can paste the sequence into the interface and output the appropriate sequence. protein aggregation, sequence, dna, rna, amyloid structure, protein analysis, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: University of Padua; Padua; Italy
Padova University Progetto di Ateneo CPDA121890;
Italian Ministry for University and Research FIRB Futuro in Ricerca RBFR08ZSXY
PMID:24848016 Free, Freely available biotools:pasta, OMICS_03861 https://bio.tools/pasta SCR_001768 PASTA 2.0, Prediction of amyloid structure aggregation 2026-09-05 06:24:39 180
Online Encyclopedia for Genetic Epidemiology studies
 
Resource Report
Resource Website
10+ mentions
Online Encyclopedia for Genetic Epidemiology studies (RRID:SCR_001825) OEGE data or information resource, portal, topical portal Portal for researchers to locate information relevant to interpretation and follow-up of human genetic epidemiological discoveries, including: a range of population and case and family genetic epidemiological studies, relevant gene and sequence databases, genetic variation databases, trait measurement, resource labs, journals, software, general information, disease genes and genetic diversity. encyclopedia, epidemiology, gene, genealogist, genetic, genetic variation, diversity, health, journal, molecular genealogy, population genetics, sequence, software, trait, genome wide association study, genotyping, phenotyping, next generation sequencing, gene association study THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-10388 SCR_001825 OEGE - Online Encyclopedia for Genetic Epidemiology studies 2026-09-05 06:24:39 12
ASPGD
 
Resource Report
Resource Website
100+ mentions
ASPGD (RRID:SCR_002047) ASPGD, ASPGD LOCUS, ASPGD REF data or information resource, data repository, database, service resource, storage service resource Database of genetic and molecular biological information about the filamentous fungi of the genus Aspergillus including information about genes and proteins of Aspergillus nidulans and Aspergillus fumigatus; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information; as well as a multispecies comparative genomics browser tool (Sybil) for exploration of orthology and synteny across multiple sequenced Sgenus species. Also available are Gene Ontology (GO) and community resources. Based on the Candida Genome Database, the Aspergillus Genome Database is a resource for genomic sequence data and gene and protein information for Aspergilli. Among its many species, the genus contains an excellent model organism (A. nidulans, or its teleomorph Emericella nidulans), an important pathogen of the immunocompromised (A. fumigatus), an agriculturally important toxin producer (A. flavus), and two species used in industrial processes (A. niger and A. oryzae). Search options allow you to: *Search AspGD database using keywords. *Find chromosomal features that match specific properties or annotations. *Find AspGD web pages using keywords located on the page. *Find information on one gene from many databases. *Search for keywords related to a phenotype (e.g., conidiation), an allele (such as veA1), or an experimental condition (e.g., light). Analysis and Tools allow you to: *Find similarities between a sequence of interest and Aspergillus DNA or protein sequences. *Display and analyze an Aspergillus sequence (or other sequence) in many ways. *Navigate the chromosomes set. View nucleotide and protein sequence. *Find short DNA/protein sequence matches in Aspergillus. *Design sequencing and PCR primers for Aspergillus or other input sequences. *Display the restriction map for a Aspergillus or other input sequence. *Find similarities between a sequence of interest and fungal nucleotide or protein sequences. AspGD welcomes data submissions. function, gene, gene name, annotation, aspergillus, aspergillus nidulans, chromosome, community, dna, genome, genomic, localization, orthology, phenotype, protein, protein-coding genes, s. cerevisiae, sequence, allele, data analysis service, bio.tools, FASEB list is used by: NIF Data Federation
is listed by: bio.tools
is listed by: Debian
is related to: Candida Genome Database
is related to: AmiGO
has parent organization: Stanford University School of Medicine; California; USA
has parent organization: Broad Institute
NIAID R01 AI077599 PMID:19773420 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-12244, biotools:aspgd http://www.aspergillusgenome.org/, https://bio.tools/aspgd SCR_002047 Aspergillus Genome Database, ASPGD REF, ASPGD LOCUS 2026-09-05 06:24:43 218
SAMTOOLS
 
Resource Report
Resource Website
10000+ mentions
SAMTOOLS (RRID:SCR_002105) SAMtools data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit Original SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data. Samtools, BCFtools, HTSlib, next generation sequencing, nucleotide alignments, sequence variant, genomic, c, perl, read, alignment, nucleotide, sequence, data, process, sam, bam, cram, vcf, bcf, bio.tools is used by: deFuse
is used by: Short Read Sequence Typing for Bacterial Pathogens
is used by: ROSE
is used by: Fcirc
is listed by: OMICtools
is listed by: Genetic Analysis Software
is listed by: SNVer
is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
is related to: Platypus
is related to: shovill
is related to: pysam
has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom
is parent organization of: SAMtools/BCFtools
is required by: RelocaTE
is required by: Wessim
is required by: SL-quant
is required by: smMIPfil
NHGRI U54 HG002750;
Wellcome Trust
PMID:19505943
PMID:21903627
DOI:10.1093/bioinformatics/btp352
Free, Available for download, Freely available SCR_018682, biotools:samtools, OMICS_01074, nlx_154607, OMICS_00090 https://github.com/samtools/samtools, https://github.com/samtools/htslib, https://bio.tools/samtools, https://sources.debian.org/src/samtools/ http://samtools.sourceforge.net/ SCR_002105 samtools, Samtools, Sequence Alignment Map TOOLS, SAMtools, SAM tools 2026-09-05 06:24:44 33299
GeneTack
 
Resource Report
Resource Website
1+ mentions
GeneTack (RRID:SCR_011953) GeneTack analysis service resource, data analysis service, data or information resource, database, production service resource, service resource Tools for frameshift prediction and a frameshift database. genomic sequence, transcript sequence, sequence, metagenomic sequence, frameshift is listed by: OMICtools
has parent organization: Georgia Institute of Technology; Georgia; USA
OMICS_01540 SCR_011953 GeneTack: tools for frameshift prediction 2026-09-05 06:27:16 1
JiffyNet
 
Resource Report
Resource Website
1+ mentions
JiffyNet (RRID:SCR_011954) analysis service resource, data analysis service, production service resource, service resource, simulation software, software application, software resource Web based instant protein network modeler for newly sequenced species. Web server designed to instantly construct genome scale protein networks using protein sequence data. Provides network visualization, analysis pages and solution for instant network modeling of newly sequenced species. protein network, protein, network, genome, sequence, pathway annotation, network visualization, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: Yonsei University; Seoul; South Korea
National Research Foundation of Korea ;
Next-Generation BioGreen 21 Program
PMID:23685435 Free, Freely available OMICS_01548, biotools:jiffynet https://bio.tools/jiffynet SCR_011954 2026-09-05 06:27:16 1
DTU Center for Biological Sequence Analysis
 
Resource Report
Resource Website
1000+ mentions
DTU Center for Biological Sequence Analysis (RRID:SCR_003590) CBS, DTU CBS analysis service resource, data access protocol, production service resource, service resource, software resource, web service Center for Biological Sequence Analysis of the Technical University of Denmark conducts basic research in the field of bioinformatics and systems biology and directs its research primarily towards topics related to the elucidation of the functional aspects of complex biological mechanisms. A large number of computational methods have been produced, which are offered to others via WWW servers. Several data sets are also available. The center also has experimental efforts in gene expression analysis using DNA chips and data generation in relation to the physical and structural properties of DNA. The on-line prediction services at CBS are available as interactive input forms. Most of the servers are also available as stand-alone software packages with the same functionality. In addition, for some servers, programmatic access is provided in the form of SOAP-based Web Services. The center also educates engineering students in biotechnology and systems biology and offers a wide range of courses in bioinformatics, systems biology, human health, microbiology and nutrigenomics. nucleotide, sequence, amino acid, dna, microarray, molecule, immunology, protein function, protein structure, protein, post-translational, whole genome, sequence analysis has parent organization: Technical University of Denmark; Lyngby; Denmark
is parent organization of: NESbase
is parent organization of: O-GLYCBASE
is parent organization of: OligoWiz
is parent organization of: SignalP
Danish National Research Foundation ;
Danish Research Councils ;
Danish Center for Scientific Computing ;
Villum Kann Rasmussen Foundation ;
Novo Nordisk Foundation ;
European Union ;
NIH
nlx_12329 http://www.cbs.dtu.dk/index.shtml SCR_003590 2026-09-05 06:25:06 1475

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