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on page 1 showing 20 out of 65 results

    Genometa

Cite this (Genometa, RRID:SCR_001181)

URL: http://genomics1.mh-hannover.de/genometa/index.php?Site=Home

Resource Type: Resource, software resource

A Java based bioinformatics program which allows rapid analysis of metagenomic short read datasets. Millions of short reads can be accurately analysed within minutes and visualised in the browser component. A large database of diverse bacteria and archaea has been constructed as a reference sequence. The approach is based upon the established open source visualisation tool IGB and supported by the rapid alignment program bowtie. The Picard toolset for SAM files is also made use of.

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Cite this ( Mucosal HIV and Immunobiology Center Genetically-Defined Microbe Core , RRID:SCR_015262)

URL: https://digestivediseasescenters.org/content/ddrc-uab-genetically-defined-microbe-core

Resource Type: Resource, service resource, resource, core facility, access service resource

Core composed of the Viral Unit, which provides labeled andn unlabeled viral components, and Bacterial Unit, which provides bacteria and bacterial proteins for research. The retroviral unit focues on the viral components of the retrovirus HIV-1.

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    ASAP

Cite this (ASAP, RRID:SCR_001849)

URL: https://omictools.com/asap-3-tool

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

Database and web interface developed to store, update and distribute genome sequence data and gene expression data. ASAP was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they move from the preliminary data stage through post-sequencing functional analysis. The ASAP database includes multiple genome sequences at various stages of analysis, and gene expression data from preliminary experiments. Use of some of this preliminary data is conditional, and it is the users responsibility to read the data release policy and to verify that any use of specific data obtained through ASAP is consistent with this policy. There are four main routes to viewing the information in ASAP: # a summary page, # a form to query the genome annotations, # a form to query strain collections, and # a form to query the experimental data. Navigational buttons appear on every page allowing users to jump to any of these four points.

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    MPIDB

Cite this (MPIDB, RRID:SCR_001898)

URL: http://www.jcvi.org/mpidb

Resource Type: Resource, data or information resource, database

Database that collects and provides all known physical microbial interactions. Currently, 24,295 experimentally determined interactions among proteins of 250 bacterial species/strains can be browsed and downloaded. These microbial interactions have been manually curated from the literature or imported from other databases (IntAct, DIP, BIND, MINT) and are linked to 26,578 experimental evidences (PubMed ID, PSI-MI methods). In contrast to these databases, interactions in MPIDB are further supported by 68,346 additional evidences based on interaction conservation, co-purification, and 3D domain contacts (iPfam, 3did). (spoke/matrix) binary interactions inferred from pull-down experiments are not included.

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Cite this (cpnDB: A Chaperonin Database, RRID:SCR_002263)

URL: http://www.cpndb.ca/cpnDB/home.php

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resource

A curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The database contains all available sequences for both group I and group II chaperonins. Users can search the database by Chaperonin type, group (I or II), BLAST, or other options, and can also enter and analyze FASTA sequences.

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Cite this (Genomes Online Database, RRID:SCR_002817)

URL: http://www.genomesonline.org/

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

Database of information regarding genome and metagenome sequencing projects, and their associated metadata, around the world. It also provides information related to organism properties such as phenotype, ecotype and disease. Both complete and ongoing projects, along with their associated metadata, can be accessed. Users can also register, annotate and publish genome and metagenome data.

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Cite this (Pathosystems Resource Integration Center, RRID:SCR_004154)

URL: http://www.patricbrc.org/portal/portal/patric/Home

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, bioinformatics resource center, data or information resource

A Bioinformatics Resource Center bacterial bioinformatics database and analysis resource that provides researchers with an online resource that stores and integrates a variety of data types (e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data) and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. The PATRIC project includes three primary collaborators: the University of Chicago, the University of Manchester, and New City Media. The University of Chicago is providing genome annotations and a PATRIC end-user genome annotation service using their Rapid Annotation using Subsystem Technology (RAST) system. The National Centre for Text Mining (NaCTeM) at the University of Manchester is providing literature-based text mining capability and service. New City Media is providing assistance in website interface development. An FTP server and download tool are available.

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    LMAT

Cite this (LMAT, RRID:SCR_004646)

URL: https://computation-rnd.llnl.gov/lmat/

Resource Type: Resource, software resource

Open-source software tool to assign taxonomic labels to as many reads as possible in very large metagenomic datasets and report the taxonomic profile of the input sample. The quick "single pass" analysis of every read allows read binning to support additional more computationally expensive analysis such as metagenomic assembly or sensitive database searches on targeted subsets of reads.

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    NBC

Cite this (NBC, RRID:SCR_004772)

URL: http://nbc.ece.drexel.edu/

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

Webserver for taxonomic classification of metagenomic reads.

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    OMPdb

Cite this (OMPdb, RRID:SCR_006221)

URL: http://aias.biol.uoa.gr/OMPdb/

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resource

A database of Beta-barrel outer membrane proteins from Gram-negative bacteria. The web interface of OMPdb offers the user the ability not only to view the available data, but also to submit advanced queries for text search within the database''s protein entries or run BLAST searches against the database. The most up-to-date version of the database (as well as all past versions) can be downloaded in various formats (flat text, XML format or raw FASTA sequences). For constructing OMPdb, multiple freely accessible resources were combined and a detailed literature search was performed. The classification of OMPdb''s protein entries into families is based mainly on structural and functional criteria. Information included in the database consists of sequence data, as well as annotation for structural characteristics (such as the transmembrane segments), literature references and links to other public databases, features that are unique worldwide. Along with the database, a collection of profile Hidden Markov Models that were shown to be characteristic for Beta-barrel outer membrane proteins was also compiled. This set, when used in combination with our previously developed algorithms (PRED-TMBB, MCMBB and ConBBPRED) will serve as a powerful tool in matters of discrimination and classification of novel Beta-barrel proteins and whole-genome analyses.

  • From Current Category

Cite this (ProLysED - Prokaryotic Lysis Enzymes Database, RRID:SCR_007183)

URL: http://www.genomemalaysia.gov.my/prolyses/

Resource Type: Resource, data or information resource, database

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 14, 2014. Database on the subject of bacterial (prokaryotic) proteases. ProLysED is a freely browsable using the Demo account. Certain services will require user registration.

  • From Current Category

Cite this (Pathogenic Disease Ontology, RRID:SCR_010405)

URL: http://purl.bioontology.org/ontology/PDO

Resource Type: Resource, ontology, data or information resource, controlled vocabulary

An ontology for describing both human infectious disease caused by bacteria and the disease that is related to bacterial infection.

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    VAAL

Cite this (VAAL, RRID:SCR_001184)

URL: http://www.broadinstitute.org/science/programs/genome-biology/computational-rd/vaal-manual

Resource Type: Resource, software resource

A polymorphism discovery algorithm for short reads. To run it, you provide reads (and quality scores) from a "sample genome" as input, along with a vector sequence to trim from the reads, and a reference sequence for a related genome to compare to. VAAL produces as output a an assembly for the sample genome, together with a mask showing which bases are "trusted". It then deduces from that a list of differences between the sample and related genomes. Alternatively, it can be provided as input read data for two sample genomes, together with a reference sequence for a related genome. In this case, VAAL produces assemblies for each of the sample genomes, and compares them to each other, thereby deducing a list of differences between them. VAAL has been tested on bacteria, using single lanes of 36 bp unpaired reads from the Illumina platform. Note: This software package is no longer supported and information on this page is provided for archival purposes only.

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    OrthoDB

Cite this (OrthoDB, RRID:SCR_011980)

URL: http://cegg.unige.ch/orthodb7

Resource Type: Resource, data or information resource, database

Database of orthologous protein-coding genes across 64 vertebrates, 57 arthropods, 175 fungi, 14 basal metazoans, and 1115 bacteria.

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    HOMD

Cite this (HOMD, RRID:SCR_012770)

URL: http://www.homd.org/index.php

Resource Type: Resource, data or information resource, database

Database of comprehensive information on the approximately 600 prokaryote species that are present in the human oral cavity. The majority of these species are uncultivated and unnamed, recognized primarily by their 16S rRNA sequences. The HOMD presents a provisional naming scheme for the currently unnamed species so that strain, clone, and probe data from any laboratory can be directly linked to a stably named reference entity. The HOMD links sequence data with phenotypic, phylogenetic, clinical, and bibliographic information. Full and partial oral bacterial genome sequences determined as part of this project and the Human Microbiome Project, are being added to the HOMD as they become available. HOMD offers easy to use tools for viewing all publicly available oral bacterial genomes. Data is also downloadable.

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Cite this (CAZy- Carbohydrate Active Enzyme, RRID:SCR_012909)

URL: http://www.cazy.org

Resource Type: Resource, data or information resource, database

Database that describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. This specialist database is dedicated to the display and analysis of genomic, structural and biochemical information on Carbohydrate-Active Enzymes (CAZymes). CAZy data are accessible either by browsing sequence-based families or by browsing the content of genomes in carbohydrate-active enzymes. New genomes are added regularly shortly after they appear in the daily releases of GenBank. New families are created based on published evidence for the activity of at least one member of the family and all families are regularly updated, both in content and in description. An original aspect of the CAZy database is its attempt to cover all carbohydrate-active enzymes across organisms and across subfields of glycosciences. One can search for CAZY Family pages using the Protein Accession (Genpept Accession, Uniprot Accession or PDB ID), Cazy family name or EC number. In addition, genomes can be searched using the NCBI TaxID. This search can be complemented by Google-based searches on the CAZy site.

  • From Current Category

Cite this (NCBI Assembly Archive Viewer, RRID:SCR_012917)

URL: http://www.ncbi.nlm.nih.gov/Traces/assembly/assmbrowser.cgi

Resource Type: Resource, data set, service resource, data or information resource

Graphical interface to contig and trace data in NCBI's Assembly Archive. The Archive links the raw sequence information found in the Trace Archive with assembly information found in publicly available sequence repositories (GenBank/EMBL/DDBJ). The Assembly Viewer allows a user to see the multiple sequence alignments as well as the actual sequence chromatogram.

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    xFITOM

Cite this (xFITOM, RRID:SCR_014445)

URL: http://erilllab.umbc.edu/research/software/xfitom/

Resource Type: Resource, standalone software, data processing software, software application, sequence analysis software, data analysis software, software resource

A fully customizable program that uses a graphical user interface to locate transcription factor-binding sites in genomic sequences. xFITOM scans DNA or RNA sequences for putative binding sites as defined by a collection of aligned known sites, a consensus sequence in IUPAC degenerate-base format, or a combination of the two.

  • From Current Category

Cite this ( Cystic Fibrosis Center - University of Washington Microbiology Core , RRID:SCR_015403)

URL: http://depts.washington.edu/cfrtc/microbiology/

Resource Type: Resource, service resource, resource, core facility, access service resource

Core facility which provides tools, reagents, and training for microbiological researchers investigating cystic fibrosis. They specifically provide resources for research in anti-bacterial therapies,

  • From Current Category

Cite this (Integrative Human Microbiome Project, RRID:SCR_015586)

URL: http://ihmpdcc.org/

Resource Type: Resource, organization portal, portal, data or information resource

Portal that serves as a common repository for diverse human microbiome datasets and minimum reporting standards. The overall mission of the HMP is to generate resources to facilitate characterization of the human microbiota to further the understanding of how the microbiome impacts human health and disease.

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