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on page 1 showing 20 out of 25 results

    CCTOP

Cite this (CCTOP, RRID:SCR_016963)

URL: http://cctop.enzim.ttk.mta.hu/

Resource Type: Resource, data access protocol, production service resource, web service, analysis service resource, service resource, software resource

Web application providing transmembrane topology prediction. Server incorporates topology information from existing experimental and computational sources using the probabilistic framework of hidden Markov model. Provides the option to precede the topology prediction with signal peptide prediction and transmembrane globular protein discrimination. Given the amino acid sequence of a putative ? helical transmembrane protein, CCTOP predicts its topology i.e. localization of membrane spanning regions and orientation of segments between them.

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Cite this (Clonotator, RRID:SCR_016730)

URL: http://ec2-52-91-98-53.compute-1.amazonaws.com/run/

Resource Type: Resource, image analysis software, data analysis software, data processing software, data access protocol, web service, software application, sequence analysis software, alignment software, software resource

Web based platform that integrates several bioinformatics tools for screening and annotation of cDNA construct sequences. Translates the nucleotide sequence of the construct into an amino acid sequence, aligns the predicted sequence to a reference database of protein sequences and identifies the best protein and isoform match, annotates any variants present in the construct, and incorporates disease-associated mutations and transcriptomic data.

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    CRISPR-P

Cite this (CRISPR-P, RRID:SCR_016941)

URL: http://crispr.hzau.edu.cn/CRISPR/

Resource Type: Resource, data access protocol, production service resource, analysis service resource, web service, service resource, software resource

Web tool for synthetic single-guide RNA design of CRISPR-system in plants. Allows to search for high specificity Cas9 target sites within DNA sequences of interest, which also provides off-target loci prediction for specificity analyses and marks restriction enzyme cutting site to every sgRNA for further convenient in experiment.

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    DIALIGN

Cite this (DIALIGN, RRID:SCR_003041)

URL: http://bibiserv.techfak.uni-bielefeld.de/dialign/

Resource Type: Resource, data analysis service, data access protocol, production service resource, analysis service resource, web service, service resource, software resource

Tool for multiple sequence alignment using various sources of external information that is particularly useful to detect local homologies in sequences with low overall similarity. While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences. No gap penalty is used. This approach can be used for both global and local alignment, but it is particularly successful in situations where sequences share only local homologies. Several versions of DIALIGN are available online at GOBICS, http://dialign.gobics.de/

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Cite this (DTU Center for Biological Sequence Analysis, RRID:SCR_003590)

URL: http://www.cbs.dtu.dk/index.shtml

Resource Type: Resource, topical portal, data access protocol, production service resource, analysis service resource, training resource, data analysis service, data set, web service, service resource, portal, software resource, data or information resource

The Center for Biological Sequence Analysis of the Technical University of Denmark conducts basic research in the field of bioinformatics and systems biology and directs its research primarily towards topics related to the elucidation of the functional aspects of complex biological mechanisms. A large number of computational methods have been produced, which are offered to others via WWW servers. Several data sets are also available. The center also has experimental efforts in gene expression analysis using DNA chips and data generation in relation to the physical and structural properties of DNA. The on-line prediction services at CBS are available as interactive input forms. Most of the servers are also available as stand-alone software packages with the same functionality. In addition, for some servers, programmatic access is provided in the form of SOAP-based Web Services. The center also educates engineering students in biotechnology and systems biology and offers a wide range of courses in bioinformatics, systems biology, human health, microbiology and nutrigenomics.

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Cite this (EMBOSSMatcher, RRID:SCR_017252)

URL: https://www.ebi.ac.uk/Tools/psa/emboss_matcher/

Resource Type: Resource, image analysis software, data processing software, data access protocol, alignment software, software application, web service, software resource

Software tool for pairwise sequence alignment. Identifies local similarities in two input sequences. One of EMBL-EBI search and sequence analysis tools.

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    Ensembl

Cite this (Ensembl, RRID:SCR_002344)

URL: http://www.ensembl.org/

Resource Type: Resource, data analysis service, data access protocol, database, web service, production service resource, analysis service resource, catalog, service resource, software resource, data or information resource

Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.

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    Entrez

Cite this (Entrez, RRID:SCR_016640)

URL: https://www.ncbi.nlm.nih.gov/Web/Search/entrezfs.html

Resource Type: Resource, web service, software resource, portal, data access protocol, data or information resource

Web portal for global query cross database search and retrieval system that provides access to all databases simultaneously with a single query string and user interface. Retrieves nucleotide and protein sequence data, gene centered and genomic mapping information, 3D structures, and references.
Covers databases including protein sequence data from PIR-International, PRF, Swiss-Prot, and PDB and nucleotide sequence data from GenBank that includes information from EMBL and DDBJ.

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    Fastml

Cite this (Fastml, RRID:SCR_016092)

URL: http://fastml.tau.ac.il/

Resource Type: Resource, web service, software resource, data access protocol, web application

Web application for the reconstruction of ancestral sequences. It computes maximum likelihood ancestral sequence reconstruction based on the phylogenetic relations between homologous sequences.

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    Gene3D

Cite this (Gene3D, RRID:SCR_007672)

URL: http://gene3d.biochem.ucl.ac.uk/Gene3D/

Resource Type: Resource, data access protocol, database, web service, service resource, storage service resource, software resource, data repository, data or information resource

A large database of CATH protein domain assignments for ENSEMBL genomes and Uniprot sequences. Gene3D is a resource of form studying proteins and the component domains. Gene3D takes CATH domains from Protein Databank (PDB) structures and assigns them to the millions of protein sequences with no PDB structures using Hidden Markov models. Assigning a CATH superfamily to a region of a protein sequence gives information on the gross 3D structure of that region of the protein. CATH superfamilies have a limited set of functions and so the domain assignment provides some functional insights. Furthermore most proteins have several different domains in a specific order, so looking for proteins with a similar domain organization provides further functional insights. Strict confidence cut-offs are used to ensure the reliability of the domain assignments. Gene3D imports functional information from sources such as UNIPROT, and KEGG. They also import experimental datasets on request to help researchers integrate there data with the corpus of the literature. The website allows users to view descriptions for both single proteins and genes and large protein sets, such as superfamilies or genomes. Subsets can then be selected for detailed investigation or associated functions and interactions can be used to expand explorations to new proteins. The Gene3D web services provide programmatic access to the CATH-Gene3D annotation resources and in-house software tools. These services include Gene3DScan for identifying structural domains within protein sequences, access to pre-calculated annotations for the major sequence databases, and linked functional annotation from UniProt, GO and KEGG.

  • From Current Category

Cite this (Genotyping, RRID:SCR_016645)

URL: https://www.ncbi.nlm.nih.gov/projects/genotyping/formpage.cgi

Resource Type: Resource, data analysis software, data processing software, data access protocol, web service, software application, sequence analysis software, software resource

Web tool to identify the genotype of a viral sequence. A window is slid along the query sequence and each window is compared by BLAST to each of the reference sequences for a particular virus.

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Cite this (InterProScan, RRID:SCR_005829)

URL: http://www.ebi.ac.uk/Tools/pfa/iprscan/

Resource Type: Resource, data analysis service, data analysis software, data processing software, data access protocol, production service resource, analysis service resource, software application, web service, service resource, software resource

Software package for functional analysis of sequences by classifying them into families and predicting presence of domains and sites. Scans sequences against InterPro's signatures. Characterizes nucleotide or protein function by matching it with models from several different databases. Used in large scale analysis of whole proteomes, genomes and metagenomes. Available as Web based version and standalone Perl version and SOAP Web Service.

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    KEGG

Cite this (KEGG, RRID:SCR_012773)

URL: http://www.kegg.jp/

Resource Type: Resource, topical portal, data access protocol, database, web service, production service resource, data analysis service, analysis service resource, service resource, portal, software resource, data or information resource

An integrated database resource consisting of 16 main databases, broadly categorized into systems information, genomic information, and chemical information. In particular, gene catalogs in the completely sequenced genomes are linked to higher-level systemic functions of the cell, the organism, and the ecosystem. Analysis tools are also available. KEGG may be used as a reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies.

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Cite this (MAKER Web Annotation Service, RRID:SCR_005318)

URL: http://www.yandell-lab.org/software/mwas.html

Resource Type: Resource, web service, software resource, service resource, data access protocol, production service resource

The MAKER Web Annotation Service (MWAS) is an easily configurable web-accessible genome annotation pipeline. It''''s purpose is to allow research groups with small to intermediate amounts of eukaryotic and prokaryotic genome sequence (i.e. BAC clones, small whole genomes, preliminary sequencing data, etc.) to independently annotate and analyze their data and produce output that can be loaded into a genome database. MWAS is build on the stand alone genome annotation pipeline MAKER, and users who wish to annotate larger datasets and whole genomes are free to download MAKER for use on their own systems. MWAS identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MWAS can also automatically train popular gene prediction algorithms for use on new genomes for which pre-existing information is limited. MAKER is a member of the Generic Model Organism Database (GMOD) project and output produced by this site can be directly used with other GMOD tools. Annotations can be directly viewed online by the user via GBrowse, JBrowse, and Apollo, or they can be downloaded for local analysis and integration into a genome database. MWAS also supplies summary statistics on sequence features via the Sequence Ontology tool SOBA. MWAS should prove especially useful for emerging model organism genome projects with minimal bioinformatics expertise and computer resources, since a user can produce final genome annotations without having to install and configure any software locally.

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Cite this (MetaLocGramN, RRID:SCR_003154)

URL: http://iimcb.genesilico.pl/MetaLocGramN/

Resource Type: Resource, data analysis service, data access protocol, production service resource, analysis service resource, web service, service resource, software resource

A tool for subcellular localization prediction of Gram-negative proteins. You can also use MetaGramLocN via SOAP. SOAP enables you to invoke our method from scripts written in your programming language of choice.

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Cite this (MOLE-BLAST, RRID:SCR_016644)

URL: https://blast.ncbi.nlm.nih.gov/moleblast/moleblast.cgi

Resource Type: Resource, data analysis software, data processing software, data access protocol, web service, software application, sequence analysis software, software resource

Software tool that helps taxonomists find closest database neighbors of submitted query sequences by generating a phylogenetic tree from BLAST results.

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    NanoPipe

Cite this (NanoPipe, RRID:SCR_016852)

URL: http://bioinformatics.uni-muenster.de/tools/nanopipe2

Resource Type: Resource, data analysis service, data access protocol, production service resource, web service, analysis service resource, service resource, software resource

Web tool for analysis of MinION (ONT) long sequencing reads. Used for analysis of reads generated by the Oxford Nanopore sequencing devices. Provides alignments to any target of interest, alignment statistics and information about polymorphisms.

  • From Current Category

Cite this (NCBI BLAST, RRID:SCR_004870)

URL: http://blast.ncbi.nlm.nih.gov/Blast.cgi

Resource Type: Resource, data analysis software, data processing software, data access protocol, web service, software application, sequence analysis software, software resource

Web search tool to find regions of similarity between biological sequences. The program compares nucleotide or protein\\tsequences to sequence databases and calculates the statistical significance.

  • From Current Category

Cite this (Nuclear Hormone Receptor Scan, RRID:SCR_016975)

URL: http://www.cisreg.ca/cgi-bin/NHR-scan/nhr_scan.cgi

Resource Type: Resource, data access protocol, production service resource, web service, analysis service resource, service resource, software resource

Web interface for computational prediction of nuclear hormone receptor binding sites in genomic sequences. Flexible Hidden Markov Model framework to allow for variable spacing and orientation of half sites. Allows for parameter modifications.

  • From Current Category

    PASC

Cite this (PASC , RRID:SCR_016642)

URL: https://www.ncbi.nlm.nih.gov/sutils/pasc/viridty.cgi

Resource Type: Resource, data access protocol, production service resource, analysis service resource, database, web service, service resource, software resource, data or information resource

Web tool for analysis of pairwise identity distribution within viral families. Used for virus sequence-based classification. Data in the system are updated every day to reflect changes in virus taxonomy and additions of new virus sequences to the public database.

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