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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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T-Coffee Resource Report Resource Website 1000+ mentions |
T-Coffee (RRID:SCR_011818) | T-Coffee | analysis service resource, data analysis service, production service resource, service resource | A multiple sequence alignment server which can align Protein, DNA and RNA sequences. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Center for Genomic Regulation; Barcelona; Spain |
PMID:10964570 DOI:10.1006/jmbi.2000.4042 |
biotools:tcoffee, OMICS_00989 | https://bio.tools/tcoffee, https://sources.debian.org/src/t-coffee/ | SCR_011818 | T-Coffee: Aligns DNA RNA or Proteins using the default T-Coffee | 2026-09-19 12:57:25 | 1157 | ||||||
|
ProbCons Resource Report Resource Website 100+ mentions |
ProbCons (RRID:SCR_011813) | ProbCons | analysis service resource, data analysis service, production service resource, service resource | Efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Stanford University; Stanford; California |
PMID:15687296 DOI:10.1101/gr.2821705 |
OMICS_00986, biotools:probcons | https://bio.tools/probcons, https://sources.debian.org/src/probcons/ | SCR_011813 | ProbCons: Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences | 2026-09-19 12:57:25 | 109 | ||||||
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Genome Database for Rosaceae Resource Report Resource Website 500+ mentions |
Genome Database for Rosaceae (RRID:SCR_012756) | data or information resource, database | GDR is a curated and integrated web-based relational database. GDR contains comprehensive data of the genetically anchored peach physical map, annotated EST databases of apple, peach, almond, cherry, rose, raspberry and strawberry, Rosaceae maps and markers and all publicly available Rosaceae sequences. Annotations of ESTs include contig assembly, putative function, simple sequence repeats, ORFs, Gene Ontology and anchored position to the peach physical map where applicable. Our integrated map viewer provides graphical interface to the genetic, transcriptome and physical mapping information. We continue to add Rosaceae map data to CMap, a web-based tool that allows users to view comparisons of genetic and physical maps. ESTs, BACs and markers can be queried by various categories and the search result sites are linked to the integrated map viewer or to the WebFPC physical map sites. In addition to browsing and querying the database, users can compare their sequences with the annotated GDR sequences via a dedicated sequence similarity server running either the BLAST or FASTA algorithm, search their sequences for microsatellites using the SSR server or assemble their ESTs using the CAP3 Server. | est, genome sequence, rosaceae, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Washington State University; Washington; USA |
nif-0000-02896, biotools:gdr | https://bio.tools/gdr | http://www.bioinfo.wsu.edu/gdr/ | SCR_012756 | GDR | 2026-09-19 12:57:27 | 662 | |||||||
|
CleanEx Resource Report Resource Website 10+ mentions |
CleanEx (RRID:SCR_012911) | data or information resource, database | CleanEx is a database which provides access to public gene expression data via unique approved gene symbols and which represents heterogeneous expression data produced by different technologies in a way that facilitates joint analysis and cross-dataset comparisons. To achieve this goal, each single gene expression experiment is regularly mapped on a permanent target identifier consisting of a physical description of the targeted RNA. There is one entry per gene. To have a complete view of the transcript and its product, we also link each entry to the corresponding protein. We further provide the genomic position of the transcription start site from EPD, when available. Otherwise we give the annotated start site position in Ensembl. | gene expression, data comparison, heterogeneous expression, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: SIB Swiss Institute of Bioinformatics |
nif-0000-02667, biotools:cleanex | https://bio.tools/cleanex | SCR_012911 | CleanEx | 2026-09-19 12:57:27 | 29 | ||||||||
|
FGENESH Resource Report Resource Website 100+ mentions |
FGENESH (RRID:SCR_011928) | FGENESH | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 10,2020. Data analysis service for Hidden Markov Model (HMM)-based gene structure prediction (multiple genes, both chains). | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:fgenesh, OMICS_01483 | https://bio.tools/fgenesh | SCR_011928 | 2026-09-19 12:57:25 | 330 | |||||||
|
HSLPred Resource Report Resource Website |
HSLPred (RRID:SCR_011972) | HSLPred | analysis service resource, data analysis service, production service resource, service resource | A support vector machine (SVM)-based method for the prediction of 4 major subcellular localization (cytoplasm, mitochondrial, nuclear and plasma membrane) of human proteins using various features such as i) amino acid composition, ii) dipeptide composition and iii) evolutionary information of proteins. | subcellular localization, protein, support vector machine, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Institute of Microbial Technology; Chandigarh; India |
PMID:15647269 | Acknowledgement requested | biotools:hslpred, OMICS_01622 | https://bio.tools/hslpred | SCR_011972 | HSLPred - A SVM-based Method for Subcellular Localization of Human Proteins | 2026-09-19 12:57:26 | 0 | |||||
|
MBGD - Microbial Genome Database Resource Report Resource Website 50+ mentions |
MBGD - Microbial Genome Database (RRID:SCR_012824) | data or information resource, database | MBGD is a database for comparative analysis of completely sequenced microbial genomes, the number of which is now growing rapidly. The aim of MBGD is to facilitate comparative genomics from various points of view such as ortholog identification, paralog clustering, motif analysis and gene order comparison. The heart of MBGD function is to create orthologous or homologous gene cluster table. For this purpose, similarities between all genes are precomputed and stored into the database, in addition to the annotations of genes such as function categories that were assigned by the original authors and motifs that were found in the translated sequence. Using these homology data, MBGD dynamically creates orthologous gene cluster table. Users can change a set of organisms or cutoff parameters to create their own orthologous grouping. Based on this cluster table, users can further analyze multiple genomes from various points of view with the functions such as global map comparison, local map comparison, multiple sequence alignment and phylogenetic tree construction. | bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: National Institute for Basic Biology; Okazaki; Japan |
nif-0000-03105, biotools:mbgd | https://bio.tools/mbgd | SCR_012824 | MBGD | 2026-09-19 12:57:27 | 62 | ||||||||
|
Mouse Genome Database Resource Report Resource Website 500+ mentions |
Mouse Genome Database (RRID:SCR_012953) | MGD | data or information resource, database | Community model organism database for laboratory mouse and authoritative source for phenotype and functional annotations of mouse genes. MGD includes complete catalog of mouse genes and genome features with integrated access to genetic, genomic and phenotypic information, all serving to further the use of the mouse as a model system for studying human biology and disease. MGD is a major component of the Mouse Genome Informatics.Contains standardized descriptions of mouse phenotypes, associations between mouse models and human genetic diseases, extensive integration of DNA and protein sequence data, normalized representation of genome and genome variant information. Data are obtained and integrated via manual curation of the biomedical literature, direct contributions from individual investigators and downloads from major informatics resource centers. MGD collaborates with the bioinformatics community on the development and use of biomedical ontologies such as the Gene Ontology (GO) and the Mammalian Phenotype (MP) Ontology. | gene, genome, genetic, chromosome, clone, cytogenetic, dna, genomic, inbred, mammalian, mouse, mutant, ortholog, phenotype, primer, protein, reagent, sequence, strain, bio.tools |
is used by: DisGeNET is listed by: Debian is listed by: bio.tools is related to: Mouse Genome Informatics (MGI) has parent organization: Jackson Laboratory |
NHGRI HG000330 | PMID:21051359 | biotools:mgi, biotools:mgd, nif-0000-10301 | http://www.informatics.jax.org/mgihome/projects/overview.shtml, https://bio.tools/mgd, https://bio.tools/mgi | SCR_012953 | Mouse Genome Informatics: Mouse Genome Database, MGID, Mouse Genome Informatics Database | 2026-09-19 12:57:27 | 545 | |||||
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PREDDIMER Resource Report Resource Website 10+ mentions |
PREDDIMER (RRID:SCR_011963) | PREDDIMER | analysis service resource, data analysis service, production service resource, service resource | Prediction tool to reconstruct putative dimer conformations for given sequences of transmembrane protein fragments, which are considered as ideal alpha-helices. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24202542 | Free | OMICS_01614, biotools:preddimer | https://bio.tools/preddimer | SCR_011963 | PREDDIMER - Prediction tool for an ensemble of transmembrane ?-helical dimer conformations | 2026-09-19 12:57:26 | 15 | |||||
|
psRNATarget Resource Report Resource Website 1000+ mentions |
psRNATarget (RRID:SCR_013321) | psRNATarget | analysis service resource, data analysis service, production service resource, service resource | A plant small RNA target analysis server which features two important analysis functions: 1) reverse complementary matching between miRNA and target transcript using a proven scoring schema, and 2) target site accessibility evaluation by calculating unpaired energy (UPE) required to ?open? secondary structure around miRNA?s target site on mRNA. PsRNATarget incorporates recent discoveries in plant miRNA target recognition, e.g. it distinguishes translational and post-transcriptional inhibition, and it reports the number of miRNA/target site pairs that may affect miRNA binding activity to target transcript. PsRNATarget is designed for high-throughput analysis of next-generation data with an efficient distributed computing back-end pipeline that runs on a Linux cluster. The server front-end integrates three simplified user-friendly interfaces to accept user-submitted or preloaded miRNAs and transcript sequences; and outputs a comprehensive list of miRNA / target pairs along with the online tools for batch downloading, key word searching and results sorting., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Samuel Roberts Noble Foundation |
PMID:21622958 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00414, biotools:psrnatarget | https://bio.tools/psrnatarget | SCR_013321 | psRNATarget: A Plant Small RNA Target Analysis Server | 2026-09-19 12:57:29 | 1117 | |||||
|
MINAS - Metal Ions in Nucleic AcidS Resource Report Resource Website 1+ mentions |
MINAS - Metal Ions in Nucleic AcidS (RRID:SCR_013145) | MINAS | data or information resource, database | Database compiling the detailed information on innersphere, outersphere and larger coordination environment of >70,000 metal ions of 36 elements found in >2000 structures of nucleic acids contained today in the PDB and NDB. MINAS is updated monthly with new structures and offers a multitude of search functions, e.g. the kind of metal ion, metal-ligand distance, innersphere and outersphere ligands defined by element or functional group, residue, experimental method, as well as PDB entry-related information. The results of each search can be saved individually for later use with so-called miniPDB files containing the respective metal ion together with the coordination environment within a 15 A radius. MINAS thus offers a unique way to explore the coordination geometries and ligands of metal ions together with the respective binding pockets in nucleic acids. | metal ion, binding pocket, nucleic acid, metal-ligand distance, innersphere ligand, outersphere ligand, ligand, element, functional group, residue, protein databank, bio.tools |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools is related to: Nucleic Acid Database is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: University of Zurich; Zurich; Switzerland |
Swiss National Science Foundation PP002-68733/1 | PMID:22096233 | nlx_151459, biotools:minas | https://bio.tools/minas | SCR_013145 | Metal Ions in Nucleic AcidS, MINAS - A Database of Metal Ions in Nucleic AcidS | 2026-09-19 12:57:28 | 5 | |||||
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GENSCAN Resource Report Resource Website 500+ mentions |
GENSCAN (RRID:SCR_013362) | genscan | analysis service resource, data analysis service, production service resource, service resource | Web server for identification of complete gene structures in genomic DNA.Tool for predicting locations and exon-intron structures of genes in genomic sequences from variety of organisms. Used for prediction of complete gene structures in human genomic DNA. | complete gene structures identyfication, genomic DNA, predicting locations, exon-intron structures, genomic sequences, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Stanford University; Stanford; California has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
PMID:9149143 | Restricted | biotools:genscan, OMICS_01494 | https://bio.tools/genscan | SCR_013362 | GENSCAN Web Server at MIT | 2026-09-19 12:57:30 | 772 | |||||
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eProbalign Resource Report Resource Website |
eProbalign (RRID:SCR_013247) | analysis service resource, data analysis service, production service resource, service resource | Data analysis service that computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities. | multiple sequence alignments, partition function posterior probabilities, bio.tools |
uses: Probalign is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: New Jersey Institute of Technology; New Jersey; USA |
NIGMS R01 GM073082 | PMID:17485479 | OMICS_00975, biotools:eprobalign | https://bio.tools/eprobalign | SCR_013247 | eProbalign web server, EProbalign | 2026-09-19 12:57:29 | 0 | ||||||
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SYFPEITHI: A Database for MHC Ligands and Peptide Motifs Resource Report Resource Website 100+ mentions |
SYFPEITHI: A Database for MHC Ligands and Peptide Motifs (RRID:SCR_013182) | SYFPEITHI | data or information resource, database | SYFPEITHI is a database comprising more than 7000 peptide sequences known to bind class I and class II MHC molecules. The entries are compiled from published reports only. It contains a collection of MHC class I and class II ligands and peptide motifs of humans and other species, such as apes, cattle, chicken, and mouse, for example, and is continuously updated. Searches for MHC alleles, MHC motifs, natural ligands, T-cell epitopes, source proteins/organisms and references are possible. Hyperlinks to the EMBL and PubMed databases are included. In addition, ligand predictions are available for a number of MHC allelic products. The database is based on previous publications on T-cell epitopes and MHC ligands. It contains information on: -Peptide sequences -anchor positions -MHC specificity -source proteins, source organisms -publication references Since the number of motifs continuously increases, it was necessary to set up a database which facilitates the search for peptides and allows the prediction of T-cell epitopes. The prediction is based on published motifs (pool sequencing, natural ligands) and takes into consideration the amino acids in the anchor and auxiliary anchor positions, as well as other frequent amino acids. The score is calculated according to the following rules: The amino acids of a certain peptide are given a specific value depending on whether they are anchor, auxiliary anchor or preferred residue. Ideal anchors will be given 10 points, unusual anchors 6-8 points, auxiliary anchors 4-6 and preferred residues 1-4 points. Amino acids that are regarded as having a negative effect on the binding ability are given values between -1 and -3. Sponsors: SYFPEITHI is supported by DFG-Sonderforschungsbereich 685 and theEuropean Union: EU BIOMED CT95-1627, BIOTECH CT95-0263, and EU QLQ-CT-1999-00713. | epitope, allele, allelic, amino acid, ape, bind, cattle, chicken, class i, class ii, human, immunological database, ligand, mhc, molecule, motif, mouse, natural, organism, peptide, product, protein, sequence, specie, t-cell, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: University of Tubingen; Tubingen; Germany |
nif-0000-21383, biotools:syfpeithi | https://bio.tools/syfpeithi | SCR_013182 | SYFPEITHI | 2026-09-19 12:57:28 | 269 | |||||||
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Cube-DB Resource Report Resource Website 1+ mentions |
Cube-DB (RRID:SCR_013233) | Cube-DB | data or information resource, database | Cube-DB is a database of pre-evaluated conservation and specialization scores for residues in paralogous proteins belonging to multi-member families of human proteins. Protein family classification follows (largely) the classification suggested by HUGO Gene Nomenclature Committee. Sets of orhtologous protein sequences were generated by mutual-best-hit strategy using full vertebrate genomes available in Ensembl. The scores, described on documentation page, are assigned to each individual residue in a protein, and presented in the form of a table (html or downloadable xls formats) and mapped, when appropriate, onto the related structure (Jmol, Pymol, Chimera). | protein, functional divergence, vertebrate, genome, ortholog, protein sequence, data set, bio.tools |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools has parent organization: Bioinformatics Institute; Singapore; Singapore |
PMID:22139934 | nlx_149432, biotools:cube-db | https://bio.tools/cube-db | SCR_013233 | Cube-DB: Detection of Functional Divergence in Human Protein Families | 2026-09-19 12:57:29 | 3 | ||||||
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e-Driver Resource Report Resource Website 1+ mentions |
e-Driver (RRID:SCR_002674) | software application, software resource, standalone software | Software tool to identify cancer driver genes based on linear annotations of biological regions such as protein domains.Uses information on three-dimensional structures of mutated proteins to identify specific structural features. Then algorithm analyzes whether these features are enriched in cancer somatic mutations and are candidate driver genes. | Identify cancer driver genes, candidate driver genes, perl, protein, mutated proteins, cancer somatic mutations, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Cancer | PMID:25064568 | Free, Available for download, Freely available | biotools:e-Driver, OMICS_05288 | https://bio.tools/e-Driver | SCR_002674 | 2026-09-19 12:57:46 | 5 | ||||||
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MRFSEQ Resource Report Resource Website |
MRFSEQ (RRID:SCR_002972) | algorithm resource, software resource | Algorithm based on a Markov random field (MRF) model that uses additional gene coexpression data to enhance differential gene expression prediction power. It is able to call differentially expressed (DE) genes but also assign confidence scores to each inferred DE gene. | markov, algorithm, gene expression, prediction algorithm, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at Riverside; California; USA |
PMID:23793751 | Free, Available for download, Freely available | biotools:mrfseq, OMICS_01309 | https://bio.tools/mrfseq | SCR_002972 | 2026-09-19 12:57:46 | 0 | |||||||
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IgBLAST Resource Report Resource Website 500+ mentions |
IgBLAST (RRID:SCR_002873) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on January 4,2023. IgBLAST was developed at NCBI to facilitate analysis of immunoglobulin V region sequences in GenBank. In addition to performing a regular BLAST search, IgBLAST has several additional functions: - Reports the germline V, D and J gene matches to the query sequence. - Annotates the immunoglobulin domains (FWR1 through FWR3). - Matches the returned hits (for databases other than germline genes) to the closest germline V genes, making it easier to identify related sequences. - Reveals the V(D)J junction details such as nucleotide homology between the ends of V(D)J segments and N nucleotide insertions. D and J gene reporting is only for nucleotide sequence search and requires a stretch of five or more nucleotide identity between the query and D or J genes. Sponsors: This resource is supported by the National Center for Biotechnology Information, a division of the U.S. National Library of Medicine. | gene, analysis, domain, homology, immunoglobulin v, nucleotide, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: NCBI |
PMID:23671333 | Free, Freely available | nif-0000-25554, biotools:igblast, OMICS_06083 | https://bio.tools/igblast, https://sources.debian.org/src/ncbi-igblast/ | SCR_002873 | IgBLAST | 2026-09-19 12:57:46 | 625 | ||||||
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GoSurfer Resource Report Resource Website 1+ mentions |
GoSurfer (RRID:SCR_005789) | GoSurfer | software application, software resource | GoSurfer uses Gene Ontology (GO) information to analyze gene sets obtained from genome-wide computations or microarray analyses. GoSurfer is a graphical interactive data mining tool. It associates user input genes with GO terms and visualizes such GO terms as a hierarchical tree. Users can manipulate the tree output by various means, like setting heuristic thresholds or using statistical tests. Significantly important GO terms resulted from a statistical test can be highlighted. All related information are exportable either as texts or as graphics. Platform: Windows compatible | gene, gene ontology, genome-wide, microarray, graph, data mining, statistical analysis, bioinformatics, genomics, gene cluster, multiple hypothesis testing, false discovery rate, bio.tools |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA has parent organization: Harvard T.H. Chan School of Public Health |
PMID:15702958 | Free for academic use | biotools:gosurfer, nlx_149268 | http://www.gosurfer.org, https://bio.tools/gosurfer | http://bioinformatics.bioen.illinois.edu/gosurfer/index.htm | SCR_005789 | 2026-09-19 12:57:51 | 2 | |||||
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BOMP: beta-barrel Outer Membrane protein Predictor Resource Report Resource Website 1+ mentions |
BOMP: beta-barrel Outer Membrane protein Predictor (RRID:SCR_007268) | software application, software resource | BOMP is a tool for prediction of beta-barrel integral outer membrane proteins. The user may submit a list of proteins, and receive a list of predicted BOMPs. The program, called the beta-barrel Outer Membrane protein Predictor (BOMP), is based on two separate components to recognize integral beta-barrel proteins. The first component is a C-terminal pattern typical of many integral beta-barrel proteins. The second component calculates an integral beta-barrel score of the sequence based on the extent to which the sequence contains stretches of amino acids typical of transmembrane -strands. To use the BOMP tool simply paste your fasta-formatted sequences into the text area, or choose a file which contains sequences. Then hit the submit button. It is possible to perform a BLAST search parallel with the predictions, which may be suitable in some cases. Using the BLAST search will however increase the running time substantially. Sponsors: This work was supported in part by grants from the Norwegian Research Council [SUP 140785/420 (GABI); FUGE/CBU151899/ISO], and the Meltzer Foundation, University of Bergen. Keywords: Beta-barrel, Membrane, Protein, Program, Software, Beta strand, Bacteria, | bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Bergen; Bergen; Norway |
biotools:bomp, nif-0000-30236 | https://bio.tools/bomp | SCR_007268 | BOMP Program | 2026-09-19 12:57:54 | 5 |
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