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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Noncoding RNA database Resource Report Resource Website 10+ mentions |
Noncoding RNA database (RRID:SCR_007815) | ncRNA | database, data or information resource | It is intended to provide information on the sequences and functions of transcripts which do not code for proteins, but perform regulatory roles in the cell. Currently, the database includes over 30,000 individual sequences from 99 species of Bacteria, Archaea and Eukaryota. The primary source of sequences included in the database was the GenBank. Additional annotation information for mouse and human ncRNAs was derived from FANTOM3 database and H-inviational Integrated Database of Annotated Human Genes version 3.4, respectively. Genome mapping information was derived from tha data available at the UCSC Genome Browser site. The sequences and annotations of small cytoplasmic RNAs from bacteria, for which annotation is lacking in the genome sequences, were derived from the Rfam database. The microRNAs or snoRNAs which were available in previous editions, as well as other housekeeping (infrastructural) RNAs (e.g. rRNA, tRNA, snRNA, SRP RNA) are not included in our database to avoid redundancy with more specialized databases which emerged in recent years. | bio.tools |
is listed by: bio.tools is listed by: Debian |
nif-0000-03183, biotools:ncrna | https://bio.tools/ncrna | SCR_007815 | Noncoding RNA database | 2026-08-06 09:27:01 | 13 | |||||||
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PhyloPat Resource Report Resource Website 1+ mentions |
PhyloPat (RRID:SCR_007851) | database, data or information resource | A database of phylogenetic patterns of evolution between 46 different species. PhyloPat uses the latest release of EnsMart (release 52), and their one-to-one, one-to-many and many-to-many orthologies. First, we stored all of the Ensembl IDs within the 46 species, and the orthologies between them. Second, we determined the evolutionary order of the studied species using the NCBI Taxonomy database. The phylogenetic tree of these species can be viewed here. Third, we used this phylogenetic tree as a starting point for building our phylogenetic lineages. For each gene in the first species (S. cerevisiae), we looked for orthologs in the other species. All orthologs were added to the phylogenetic lineage, and in the next round were checked for orthologs themselves, until no more orthologies were found for any of the genes. This process was repeated for all genes in all species that were not connected to any phylogenetic lineage yet. The complete phylogenetic lineage determination generated 329,998 phylogenetic lineages, consisting of 973,821 genes. These lineages can be queried here by phylogenetic patterns, MySQL regular expressions or simply a list of Ensembl/EMBL/EntrezGene/HGNC IDs. Output can be given in HTML, Excel or plain text format. | bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Radboud University; Nijmegen; The Netherlands |
nif-0000-03282, biotools:phylopat | https://bio.tools/phylopat | SCR_007851 | PhyloPat | 2026-08-06 09:27:00 | 2 | ||||||||
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PhylomeDB Resource Report Resource Website 50+ mentions |
PhylomeDB (RRID:SCR_007850) | database, data or information resource | Database for phylomes, that is, complete collections of phylogenetic trees for all proteins encoded in a given genome. It aims at providing a repository of high-quality phylogenies and alignments for proteins encoded in model species. To derive a phylome, each protein encoded in a given genome is used as a seed to retrieve its homologs in other complete genomes. These sequences are aligned and processed to derive reliable phylogenies using several phylogenetic methods. Besides providing the evolutionary history of the gene families, phylomeDB includes phylogeny based predictions of orthology and paralogy relationships., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Genome-wide collections, gene phylogenies, phylogenetic trees collection, proteins encoded, genome, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools |
PMID:17962297 PMID:21075798 PMID:24275491 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03281, biotools:PhylomeDb | https://bio.tools/PhylomeDB | SCR_007850 | PhylomeDB | 2026-08-06 09:27:01 | 52 | ||||||
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PartiGeneDB Resource Report Resource Website 1+ mentions |
PartiGeneDB (RRID:SCR_007848) | database, data or information resource | A publicly available database resource containing the assembled partial genomes for ~700 eukaryotic organisms. Partial genomes are generated from expressed sequence tag datasets containing more than 1000 sequences. PartiGeneDB allows users to view sets of genes and identify genes of interest in organisms for which a full genome is not currently available. PartiGeneDB is automatically updated to include new organism datasets as they are generated. PartiGeneDB provides four portals of entry into the database. It is hosted and supported by the Hospital for Sick Children, Toronto. In addition to providing a comprehensive resource facilitating comparative analyses, PartiGeneDB allows researchers to access the partial genomes of organisms that may not be available elsewhere. However, we recommend and encourage users interested in exploring datasets from a single organism in more depth, that you visit the specific web sites associated with the sequencing effort associated with that organism . | est, eukaryotic genome, expressed sequence tag, partial genome, bio.tools |
is listed by: bio.tools is listed by: Debian |
nif-0000-03244, biotools:partigenedb | https://bio.tools/partigenedb | SCR_007848 | PartiGeneDB | 2026-08-06 09:27:00 | 6 | ||||||||
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MetaCyc Resource Report Resource Website 1000+ mentions |
MetaCyc (RRID:SCR_007778) | MetaCyc | database, data or information resource | MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways. MetaCyc contains more than 1,200 pathways from more than 1,600 different organisms, and is curated from the scientific experimental literature. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated compounds, enzymes, and genes. | bio.tools, FASEB list |
uses: Pathway Tools is listed by: BioCyc is listed by: bio.tools is listed by: Debian is related to: BioCyc is related to: ENZYME is related to: NCBI BioSystems Database is related to: Algal Functional Annotation Tool is related to: Pathway Tools has parent organization: Stanford Research Institute International works with: MiMeDB |
r3d100011294, nif-0000-03114, biotools:metacyc | https://bio.tools/metacyc, https://doi.org/10.17616/R32K7X | SCR_007778 | 2026-08-06 09:26:58 | 1761 | ||||||||
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MEROPS Resource Report Resource Website 500+ mentions |
MEROPS (RRID:SCR_007777) | MEROPS, MEROPS fam | database, data or information resource | An information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. The MEROPS database uses an hierarchical, structure-based classification of the peptidases. In this, each peptidase is assigned to a Family on the basis of statistically significant similarities in amino acid sequence, and families that are thought to be homologous are grouped together in a Clan. There is a Summary page for each family and clan, and these have indexes. Each of the Summary pages offers links to supplementary pages. About 3000 individual peptidases and inhibitors are included in the database, and there is a Summary page describing each one. You can navigate to this by any of several routes. There are indexes of Name, MEROPS Identifier and source Organism on the menu bar. Each Summary page describes the classification and nomenclature of the peptidase or inhibitor, and provides links to supplementary pages showing sequence identifiers, the structure if known, literature references and more. | peptidase, protease, proteinase, proteolytic enzyme, protein, inhibitor, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: TopFIND has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust WT077044/Z/05/Z | PMID:19892822 | biotools:merops, r3d100012783, nif-0000-03112 | https://bio.tools/merops, https://doi.org/10.17616/R33225, https://doi.org/10.17616/R33225 | SCR_007777 | MEROPS- the Peptidase Database, MEROPS - the Peptidase Database, MEROPS database, MEROPS fam | 2026-08-06 09:26:58 | 736 | |||||
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LOCATE: subcellular localization database Resource Report Resource Website 50+ mentions |
LOCATE: subcellular localization database (RRID:SCR_007763) | database, data or information resource | LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of proteins from the RIKEN FANTOM4 mouse and human protein sequence set. The membrane organization is predicted by the high-throughput, computational pipeline MemO. The subcellular locations were determined by a high-throughput, immunofluorescence-based assay and by manually reviewing peer-reviewed publications. | bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: University of Queensland; Brisbane; Australia |
nif-0000-03086, biotools:locate | https://bio.tools/locate | SCR_007763 | LOCATE | 2026-08-06 09:26:58 | 66 | ||||||||
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VFDB - Virulence Factors of Bacterial Pathogens Resource Report Resource Website 100+ mentions |
VFDB - Virulence Factors of Bacterial Pathogens (RRID:SCR_007969) | VFDB | database, data or information resource | An integrated and comprehensive database of virulence factors for bacterial pathogens (also including Chlamydia and Mycoplasma). VFDB is a platform for further study of comparative pathogenomics. Major features include tabular comparison of pathogenomic composition in terms of virulence, multiple alignments and statistic analysis of homologous virulence genes, and graphical comparison of pathogenomic organization of VFs. Category: Genomics Databases (non-vertebrate) Subcategory: Prokaryotic genome databases | bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian |
nif-0000-03627, biotools:vfdb | https://bio.tools/vfdb | SCR_007969 | Virulence Factors of Bacterial Pathogens | 2026-08-06 09:27:03 | 483 | |||||||
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TDR Targets Database Resource Report Resource Website 10+ mentions |
TDR Targets Database (RRID:SCR_007963) | database, data or information resource | This database functions both as a website where researchers can look for information on their targets of interest; and as a tool for prioritization of targets in whole genomes. Using the database as a tool, researchers can quickly prioritize a genome of interest by performing any number of individual queries on a species of interest, then assigning numerical weights to each query (in the history page) to finally obtain a ranked list of genes by combining the weighted queries. This site is part of a WHO/TDR project seeking to exploit the availability of diverse datasets to facilitate the identification and prioritization of drug targets in pathogens causing neglected diseases. | bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian |
nif-0000-03542, biotools:tdr_targets | https://bio.tools/tdr_targets | SCR_007963 | TDR Targets | 2026-08-06 09:27:02 | 43 | ||||||||
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RNA Virus Database Resource Report Resource Website |
RNA Virus Database (RRID:SCR_007899) | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. It is a database and web application describing the genome organization and providing analytical tools for the 938 known species of RNA virus. It can identify submitted nucleotide sequences, can place them into multiple whole-genome alignments (in species where more than one isolate has been fully sequenced) and contains translated genome sequences for all species. It has been created for two main purposes: to facilitate the comparative analysis of RNA viruses and to become a hub for other, more specialised virus Web sites. | bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Oxford; Oxford; United Kingdom |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:rnavirusdb | https://bio.tools/rnavirusdb | http://virus.zoo.ox.ac.uk/rnavirusdb/ | SCR_007899 | RNA Virus Database | 2026-08-06 09:27:02 | 0 | ||||||
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Alternate splicing gallery Resource Report Resource Website 1+ mentions |
Alternate splicing gallery (RRID:SCR_008129) | database, data or information resource | Alternative splicing essentially increases the diversity of the transcriptome and has important implications for physiology, development and the genesis of diseases. This resource uses a different approach to investigate alternative splicing (instead of the conventional case-by case fashion) and integrates all transcripts derived from a gene into a single splicing graph. ASG is a database of splicing graphs for human genes, using transcript information from various major sources (Ensembl, RefSeq, STACK, TIGR and UniGene). Each transcript corresponds to a path in the graph, and alternative splicing is displayed by bifurcations. This representation preserves the relationships between different splicing variants and allows us to investigate systematically all possible putative transcripts. Web interface allows users to display the splicing graphs, to interactively assemble transcripts and to access their sequences as well as neighboring genomic regions. ASG also provide for each gene, an exhaustive pre-computed catalog of putative transcriptsin total more than 1.2 million sequences. It has found that ~65 of the investigated genes show evidence for alternative splicing, and in 5 of the cases, a single gene might produce over 100 transcripts. | gallery, gene, genesis, alternative, development, disease, diversity, genomic, human, physiology, putative transcript, sequence, single, splice, splicing graph, transcript, transcriptome, variant, bio.tools |
is listed by: bio.tools is listed by: Debian |
nif-0000-20932, biotools:alternative_splicing_gallery | https://bio.tools/alternative_splicing_gallery | SCR_008129 | ASG | 2026-08-06 09:27:06 | 1 | ||||||||
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Placnet Resource Report Resource Website |
Placnet (RRID:SCR_024176) | software library, software toolkit, software resource | Software Perl tools for plasmid analysis in NGS projects.Identifies, visualizes and analyzes plasmids in WGS projects by creating a network of contig interactions, thus allowing comprehensive plasmid analysis within WGS datasets.Optimized to work with Illumina sequences but it also works with 454, Iontorrent or any of the actual sequence technologies. The input of placnet is a set of contigs and one or more SAM files with the mapping of the reads against the contigs. Placnet obtains a set of files, easily opened on Cytoscape software or other network tools. | plasmid constellation networks, identifies splasmids, visualizes and analyzes plasmids, WGS projects, creating network of contig interactions, comprehensive plasmid analysis within WGS datasets, | is listed by: Debian | PMID:25522143 | Free, Available for download, Freely available, | OMICS_11487 | https://sources.debian.org/src/placnet/ | SCR_024176 | plasmid constellation networks, placnet | 2026-08-06 09:30:20 | 0 | ||||||
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PRINSEQ Resource Report Resource Website 50+ mentions |
PRINSEQ (RRID:SCR_024178) | software library, software toolkit, software resource | Software Perl application for quality control and data preprocessing of genomic and metagenomic datasets. Used to filter, reformat, or trim genomic and metagenomic sequence data. Generates summary statistics of sequences in graphical and tabular format. | data quality control, data preprocessing, genomic and metagenomic datasets, | is listed by: Debian | PMID:21278185 | Free, Available for download, Freely available, | https://sources.debian.org/src/prinseq-lite/ | SCR_024178 | prinseq-lite | 2026-08-06 09:30:17 | 72 | |||||||
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POA Resource Report Resource Website |
POA (RRID:SCR_024172) | software library, software toolkit, software resource | Software application for multiple sequence alignment in bioinformatics. Has superior ability to handle branching / indels in the alignment. | sequence alignment, multiple sequence alignment, handle branching in alignment, handle indels in alignment, | is listed by: Debian | DOI:10.1093/bioinformatics/bth126 | Free, Available for download, Freely available, | OMICS_14254 | https://sources.debian.org/src/poa/ | SCR_024172 | poa, Partial Order Alignment | 2026-08-06 09:30:20 | 0 | ||||||
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PLIP Resource Report Resource Website 100+ mentions |
PLIP (RRID:SCR_024173) | software library, software toolkit, software resource | Software application as protein�ligand interaction profiler to identify non-covalent interactions between biological macromolecules and their ligands. Provides atom level information on binding characteristics as well as publication ready visualizations and parsable output files. PLIP web tool is based on PLIP command line tool and offers graphical interface for analysis of few structures. | Protein Ligand Interaction Profiler, | is listed by: Debian | DOI:10.1093/nar/gkv315 | Free, Available for download, Freely available, | OMICS_08028 | https://sources.debian.org/src/plip/, https://github.com/pharmai/plip | SCR_024173 | Protein-Ligand Interaction Profiler, plip | 2026-08-06 09:30:16 | 109 | ||||||
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CiftiLib Resource Report Resource Website |
CiftiLib (RRID:SCR_023996) | software library, software toolkit, software resource | Software C++ Library for reading and writing CIFTI-2 and CIFTI-1 files. | C++, reading and writing files, CIFTI-2, CIFTI-1 | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/ciftilib/ | SCR_023996 | ciftilib | 2026-08-06 09:30:14 | 0 | ||||||||
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rapmap Resource Report Resource Website 1+ mentions |
rapmap (RRID:SCR_024204) | software library, software toolkit, software resource | Software tool for mapping RNA-seq reads to transcriptomes. Used for rapid sensitive and accurate read mapping via quasi-mapping | mapping RNA-seq reads to transcriptomes, mapping RNA-seq reads, | is listed by: Debian | PMID:27307617 | Free, Available for download, Freely available, | OMICS_10349 | https://sources.debian.org/src/rapmap/ | SCR_024204 | RapMap | 2026-08-06 09:30:17 | 9 | ||||||
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Bioparser Resource Report Resource Website 1+ mentions |
Bioparser (RRID:SCR_024065) | software library, software toolkit, software resource | Software C++ library for parsing several formats in bioinformatics. C++ header only parsing library for several bioinformatics formats (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files. | C ++, parsing formats, FASTA/Q, MHAP/PAF/SAM, support for zlib compressed files, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbioparser-dev/ | SCR_024065 | bioparser, libbioparser-dev | 2026-08-06 09:30:15 | 3 | ||||||||
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pyFAI Resource Report Resource Website 1+ mentions |
pyFAI (RRID:SCR_024186) | software library, software toolkit, software resource | Open source Python software package designed to perform azimuthal integration and, correspondingly, two-dimensional regrouping on area-detector frames for small- and wide-angle X-ray scattering experiments. | perform azimuthal integration, two-dimensional regrouping, area detector frames for small and wide angle X-ray scattering experiments, | is listed by: Debian | PMID:25844080 | Free, Available for download, Freely available, | https://sources.debian.org/src/pyfai/ | SCR_024186 | pyfai, pyFai | 2026-08-06 09:30:20 | 7 | |||||||
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BioD Resource Report Resource Website 1+ mentions |
BioD (RRID:SCR_024062) | software library, software toolkit, software resource | Software memory efficient bioinformatics library written in D programming language whose aim is to provide platform for developing high performance computational biology applications using the D programming language through automatic parallelization of tasks where possible and by avoiding unnecessary memory allocations. | D library, computational biology and bioinformatics, libbiod, biod, D programming language, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_20057 | https://sources.debian.org/src/libbiod/, https://biod.github.io/ | SCR_024062 | BioD | 2026-08-06 09:30:15 | 2 |
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