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http://merops.sanger.ac.uk/

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.

Proper citation: MEROPS (RRID:SCR_007777) Copy   

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http://locate.imb.uq.edu.au/

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.

Proper citation: LOCATE: subcellular localization database (RRID:SCR_007763) Copy   

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http://www.cmbi.ru.nl/phylopat

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.

Proper citation: PhyloPat (RRID:SCR_007851) Copy   

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http://phylomedb.bioinfo.cipf.es

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.

Proper citation: PhylomeDB (RRID:SCR_007850) Copy   

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http://www.partigenedb.org/

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 .

Proper citation: PartiGeneDB (RRID:SCR_007848) Copy   

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http://www.mgc.ac.cn/VFs/

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

Proper citation: VFDB - Virulence Factors of Bacterial Pathogens (RRID:SCR_007969) Copy   

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http://tdrtargets.org/

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.

Proper citation: TDR Targets Database (RRID:SCR_007963) Copy   

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http://bioafrica.mrc.ac.za/rnavirusdb/

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.

Proper citation: RNA Virus Database (RRID:SCR_007899) Copy   

•   Source: SciCrunch Registry

http://statgen.ncsu.edu/asg/

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.

Proper citation: Alternate splicing gallery (RRID:SCR_008129) Copy   

•   Source: SciCrunch Registry

http://swift.cmbi.ru.nl/gv/pdbfinder/

It is a very information rich protein structure database. Unfortunately, the PDB people are not very good at making their data available for search engines. There are several reasons why search engines often fail on the PDB: * The PDB has zillions of small administrative errors * The PDB-format is search-engine unfriendly * Many PDB files are incomplete The PDBFINDER project is a possible solution to these problems. The PDBFINDER holds for each PDB file a structured, search-engine-friendly-formatted entry that holds the data-items most likely needed for people search for certain types of PDB entries. The PDBFINDER is not useful to search in atomic coordinates; it is meant to ad searches in the administrative records of PDB files. Originally, the PDBFINDER was just for searching in PDB files. However, as all the time more people are using the PDBFINDER to aid modelling and database projects, they decided to also produce the so-called PDBFINDER2. The PDBFINDER2 also holds a lot of quality information about the PDB entries. Please only use the PDBFINDER2 if you really need that quality determination aspect because the PDBFINDER2 is five times bigger than the original PDBFINDER.

Proper citation: PDB Finder (RRID:SCR_008284) Copy   

•   Source: SciCrunch Registry

https://gemini.readthedocs.io/en/latest/

Framework for exploring genetic variation in the context of the genome annotations available for the human genome. Users can load a VCF file into a database and each variant is automatically annotated by comparing it to several genome annotations from source such as ENCODE tracks, UCSC tracks, OMIM, dbSNP, KEGG, and HPRD.

Proper citation: GEMINI (RRID:SCR_014819) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/package=RNeXML

Software R package provides access to phyloinformatic data in 'NeXML' format.

Proper citation: rnexml (RRID:SCR_024291) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/package=phylobase

Software R package provides base S4 class for comparative methods, incorporating one or more trees and trait data. Used for phylogenetic analysis.

Proper citation: phylobase (RRID:SCR_024292) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/qqman/index.html

Software R package to create Q-Q and manhattan plots for GWAS data from PLINK output files.

Proper citation: qqman (RRID:SCR_024293) Copy   

•   Source: SciCrunch Registry

https://synonym.caltech.edu/software/sbmltoolbox/

Software toolbox provides set of basic functions allowing SBML models to be used in both MATLAB and Octave.

Proper citation: sbmltoolbox (RRID:SCR_024329) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/package=tigger

Software R package infers V genotype of individual from immunoglobulin repertoire sequencing data like AIRR-Seq, Rep-Seq. Includes detection of any novel alleles. This information is then used to correct existing V allele calls from among sample sequences.

Proper citation: tigger (RRID:SCR_024310) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/package=wavethresh

Software R package to perform 1, 2 and 3D real and complex-valued wavelet transforms, nondecimated transforms, wavelet packet transforms, nondecimated wavelet packet transforms, multiple wavelet transforms, complex-valued wavelet transforms, wavelet shrinkage for various kinds of data, locally stationary wavelet time series, nonstationary multiscale transfer function modeling, density estimation.

Proper citation: wavethresh (RRID:SCR_024311) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/package=WebGestaltR

Software R package to support gene set enrichment analysis, network topology analysis.Can be integrated into other pipeline or simultaneously analyze multiple gene lists. The user-friendly output report allows interactive and efficient exploration of enrichment results.

Proper citation: webgestaltr (RRID:SCR_024312) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/sjPlot/index.html

Software R package as collection of plotting and table output functions for data visualization. Results of various statistical analyses that are commonly used in social sciences can be visualized using this package, including simple and cross tabulated frequencies, histograms, box plots, generalized linear models, mixed effects models, principal component analysis and correlation matrices, cluster analyses, scatter plots, stacked scales, effects plots of regression models including interaction terms. This package supports labelled data.

Proper citation: sjplot (RRID:SCR_024307) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/package=waveslim

Software R package for basic wavelet routines for time series 1D, image 2D and array 3D analysis.

Proper citation: waveslim (RRID:SCR_024308) Copy   

•   Source: SciCrunch Registry