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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
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
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
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
Data analysis service that allows to process CEL files from Affymetrix, Inc. GeneChip Gene 1.0 ST Arrays to identify alternative splicing.
Proper citation: Gene Array Analyzer (RRID:SCR_008323) Copy
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
http://www.imtech.res.in/raghava/bhairpred/
Bhairpred server is based on machine learning technique SVM using single sequence information, evolutionary profile, predicted and observed secondary structure (as obtained using Psipred and DSSP), predicted and observed accessibility values (as obtainned from Netasa and DSSP). The methods were trained and tested on dataset of 2880 proteins and their performance was evaluated on dataset of 534 proteins used by Thornton (PNAS, 2002). Best prediction results were obtained with hybrid approach that combined prediction results from evolutionary profile, predicted secondary structure and accessibility.
Proper citation: SVM based method for predicting beta hairpin structures in proteins (RRID:SCR_008349) Copy
http://array.mbb.yale.edu/analysis/
A fully integrated platform for processing microarray data.
Proper citation: ExpressYourself (RRID:SCR_008881) Copy
http://lemur.amu.edu.pl/share/php/mirnest/home.php
A database of animal, plant and virus microRNA data maintained at the University of Poznan. The database provides: * 9980 miRNA candiates from 420 animal and plant species predicted in Expressed Sequence Tags * predicted targets for plant candidates * RNA-seq reads mapped to candidates from 29 species * external data from 12 databases that includes sequences, polymorphism, expression and regulation. miRNEST 1.0, it contains miRNA from 563 animals, plants and viruses plant species.
Proper citation: miRNEST (RRID:SCR_008907) Copy
http://cbdb.nimh.nih.gov/microsniper/
A web-based application which predicts the impact of a SNP on putative microRNA targets.
Proper citation: MicroSNiPer (RRID:SCR_009880) Copy
A free, simple to use web service dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences. Phylogeny.fr runs and connects various bioinformatics programs to reconstruct a robust phylogenetic tree from a set of sequences.
Proper citation: Phylogeny.fr (RRID:SCR_010266) Copy
hiPathDB is an integrated pathway database that combines the curated human pathway data of NCI-Nature PID, Reactome, BioCarta and KEGG. In total, it includes 1661 pathways consisting of 8976 distinct physical entities. (2010.03.09) hiPathDB provides two different types of integration. The pathway-level integration, conceptually a simple collection of individual pathways, was achieved by devising an elaborate model that takes distinct features of four databases into account and subsequently reformatting all pathways in accordance with our model. The entity-level integration creates a single unified pathway that encompasses all pathways by merging common components. Even though the detailed molecular-level information such as complex formation or post-translational modifications tends to be lost, such integration makes it possible to investigate signaling network over the entire pathways and allows identification of pathway cross-talks. Another strong merit of hiPathDB is the built-in pathway visualization module that supports explorative studies of complex networks in an interactive fashion. The layout algorithm is optimized for virtually automatic visualization of the pathways.
Proper citation: hiPathDB - human integrated Pathway DB with facile visualization (RRID:SCR_008900) Copy
http://www.medinfopoli.polimi.it/GFINDer/
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 16, 2019. Multi-database system providing large-scale lists of user-classified sequence identifiers with genome-scale biological information and functional profiles biologically characterizing the different gene classes in the list. GFINDer automatically retrieves updated annotations of several functional categories from different sources, identifies the categories enriched in each class of a user-classified gene list, and calculates statistical significance values for each category. Moreover, GFINDer enables to functionally classify genes according to mined functional categories and to statistically analyze the obtained classifications, aiding in better interpreting microarray experiment results.
Proper citation: GFINDer: Genome Function INtegrated Discoverer (RRID:SCR_008868) Copy
http://centre.bioinformatics.zj.cn/mirtools/
A comprehensive web server developed to allow researchers to comprehensively characterize small RNA transcriptome.
Proper citation: mirTools (RRID:SCR_009701) Copy
A curated knowledge base of the circuitry of the hippocampus of normal adult, or adolescent, rodents at the mesoscopic level of neuronal types. Knowledge concerning dentate gyrus, CA3, CA2, CA1, subiculum, and entorhinal cortex is distilled from published evidence and is continuously updated as new information becomes available. Each reported neuronal property is documented with a pointer to, and excerpt from, relevant published evidence, such as citation quotes or illustrations. Please note: This is an alpha-testing site. The content is still being vetted for accuracy and has not yet undergone peer-review. As such, it may contain inaccuracies and should not (yet) be trusted as a scholarly resource. The content does not yet appear uniformly across all combinations of browsers and screen resolutions.
Proper citation: Hippocampome.org (RRID:SCR_009023) Copy
Ratings or validation data are available for this resource
Human and mouse genome annotation project which aims to identify all gene features in the human genome using computational analysis, manual annotation, and experimental validation.
Proper citation: GENCODE (RRID:SCR_014966) Copy
Data processing software that performs X-ray diffraction data processing. It handles multi-pass, multi-wavelength data sets and supports remote access to synchrotron facilities.
Proper citation: xia2 pipeline (RRID:SCR_015746) Copy
http://cab.spbu.ru/software/rnaquast/
Software tool for evaluating RNA-Seq assembly quality and benchmarking transcriptome assemblers using reference genome and gene database. Capable to estimate gene database coverage by raw reads and de novo quality assessment using third party software.
Proper citation: rnaQUAST (RRID:SCR_016994) Copy
http://www.splashground.de/~andy/programs/FFindex/
Database and index for huge amounts of small files. Files are stored concatenated in one big data file, with second file contains plain text index, giving name, offset and length of small files.
Proper citation: Ffindex (RRID:SCR_016110) Copy
Software designed for analysis of microscopy data. It performs sub-pixel precision detection, quantification of cells and fluorescence signals, as well as other image analysis functions.
Proper citation: Oufti (RRID:SCR_016244) Copy
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