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on page 1 showing 20 out of 25 results

Cite this (AnimalTFDB, RRID:SCR_001624)

URL: http://www.bioguo.org/AnimalTFDB/

Resource Type: Resource, data or information resource, database

A comprehensive transcription factor (TF) database in which they identified and classified all the genome-wide TFs in 50 sequenced animal genomes (Ensembl release version 60). In addition to TFs, it also collects transcription co-factors and chromatin remodeling factors of those genomes, which play regulatory roles in transcription. Here they defined the TFs as proteins containing a sequence-specific DNA-binding domain (DBD) and regulating target gene expression. Currently, the AnimalTFDB classifies all the animal TFs into 72 families according to their conserved DBDs. Gene lists of transcription factors, transcription co-factors and chromatin remodeling factors of each species are available for downloading.

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Cite this (Autophagy Database, RRID:SCR_002671)

URL: http://www.tanpaku.org/autophagy/

Resource Type: Resource, data or information resource, database

Database that provides basic, up-to-date information on relevant literature, and a list of autophagy-related proteins and their homologs in eukaryotes.

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Cite this (AutoPrime, RRID:SCR_000097)

URL: http://www.autoprime.de/AutoPrimeWeb

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

Server to rapidly design primers for real-time PCR measurement of eukaryotic expression.

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    CELLO

Cite this (CELLO, RRID:SCR_011968)

URL: http://cello.life.nctu.edu.tw/

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

A subCELlular LOcalization predictor based on a multi-class support vector machine (SVM) classification system. CELLO uses 4 types of sequence coding schemes: the amino acid composition, the di-peptide composition, the partitioned amino acid composition and the sequence composition based on the physico-chemical properties of amino acids. They combine votes from these classifiers and use the jury votes to determine the final assignment.

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Cite this (Cell-PLoc, RRID:SCR_011966)

URL: http://www.csbio.sjtu.edu.cn/bioinf/Cell-PLoc/

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

A package of web-servers for predicting subcellular localization of proteins in different organisms.

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    ChIPBase

Cite this (ChIPBase, RRID:SCR_005404)

URL: http://deepbase.sysu.edu.cn/chipbase/

Resource Type: Resource, data or information resource, database

A database for decoding transcription factor binding maps, expression profiles and transcriptional regulation of long non-coding RNAs (lncRNAs, lincRNAs), microRNAs, other ncRNAs (snoRNAs, tRNAs, snRNAs, etc.) and protein-coding genes from ChIP-Seq data. ChIPBase currently includes millions of transcription factor binding sites (TFBSs) among 6 species. ChIPBase provides several web-based tools and browsers to explore TF-lncRNA, TF-miRNA, TF-mRNA, TF-ncRNA and TF-miRNA-mRNA regulatory networks.

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    COG

Cite this (COG, RRID:SCR_007139)

URL: http://www.ncbi.nlm.nih.gov/COG

Resource Type: Resource, data or information resource, database

A database for phylogenetic classification for proteins encoded in complete genomes. Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain. Please be aware that COGs hasn't been updated in many years and will not be.

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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 (DBD: Transcription factor prediction database, RRID:SCR_002300)

URL: http://www.transcriptionfactor.org/index.cgi?Home

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

Database of predicted transcription factors in completely sequenced genomes. The predicted transcription factors all contain assignments to sequence specific DNA-binding domain families. The predictions are based on domain assignments from the SUPERFAMILY and Pfam hidden Markov model libraries. Benchmarks of the transcription factor predictions show they are accurate and have wide coverage on a genomic scale. The DBD consists of predicted transcription factor repertoires for 930 completely sequenced genomes.

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Cite this (Eukaryotic Promoter Database, RRID:SCR_002485)

URL: http://www.epd.isb-sib.ch/

Resource Type: Resource, data or information resource, database

Database for an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis.

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Cite this (Euk-mPLoc, RRID:SCR_011971)

URL: http://www.csbio.sjtu.edu.cn/bioinf/euk-multi-2/

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

Data analysis service for predicting subcellular localization of eukaryotic proteins including those with multiple sites. Euk-mPLoc covers 22 eukaryotic subcellular locations.

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    GeneTack

Cite this (GeneTack, RRID:SCR_011953)

URL: http://topaz.gatech.edu/GeneTack/cgi/print_page.cgi?fn=db_home.html&title=Frameshift%20Database

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

Tools for frameshift prediction and a frameshift database.

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Cite this (Genomicus, RRID:SCR_011791)

URL: http://www.genomicus.biologie.ens.fr/genomicus-72.01/cgi-bin/search.pl

Resource Type: Resource, data or information resource, database

A genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.

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Cite this (JGI Genome Portal, RRID:SCR_002383)

URL: http://genome.jgi.doe.gov/

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

Portal providing access to all JGI genomic databases and analytical tools, sequencing projects and their status, search for and download assemblies and annotations of sequenced genomes, and interactively explore those genomes and compare them with other sequenced microbes, fungi, plants or metagenomes using specialized systems tailored to each particular class of organisms. The Department of Energy (DOE) Joint Genome Institute (JGI) is a national user facility with massive-scale DNA sequencing and analysis capabilities dedicated to advancing genomics for bioenergy and environmental applications. Beyond generating tens of trillions of DNA bases annually, the Institute develops and maintains data management systems and specialized analytical capabilities to manage and interpret complex genomic data sets, and to enable an expanding community of users around the world to analyze these data in different contexts over the web.

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Cite this (KnowPredsite, RRID:SCR_011974)

URL: http://bio-cluster.iis.sinica.edu.tw/kbloc/index.html

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

A knowledge-based data analysis service to predict the localization site(s) of both single-localized and multi-localized proteins.

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    mGOASVM

Cite this (mGOASVM, RRID:SCR_013098)

URL: http://bioinfo.eie.polyu.edu.hk/mGoaSvmServer/mGOASVM.html

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

Data analysis service for the prediction of multi-label protein subcellular localization based on gene ontology and support vector machines. Web services are also available.

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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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    Psort

Cite this (Psort, RRID:SCR_007038)

URL: http://www.psort.org

Resource Type: Resource, topical portal, data analysis software, data processing software, production service resource, analysis service resource, software application, data analysis service, data set, service resource, portal, software resource, data or information resource

Portal to the PSORT family of computer programs for the prediction of protein localization sites in cells, as well as other datasets and resources relevant to localization prediction. The standalone versions are available for download for larger analyses.

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    PTMcode

Cite this (PTMcode, RRID:SCR_002046)

URL: http://ptmcode.embl.de/

Resource Type: Resource, data or information resource, database

Database of known and predicted functional associations between protein posttranslational modifications (PTMs) within proteins. In its first release it contains 13 different PTM types. PTM types are abbreviated in a two letter code as: Ph (phosphorylation), NG (N-linked glycosylation), Ac (acetylation), OG (O-linked glycosylation), Ub (ubiquitination), Me (methylation), SM (SUMOylation), Hy (hydroxylation), Ca (carboxylation), Pa (palmitoylation), Su (sulfation), Ni (nitrosylation) and CG (C-linked glycosylation). These PTMs are present in 25,765 proteins of 8 different eukaryotes. The database is focused on the exploration of the global post-translational regulation of proteins, not only by describing the set of its modifications, but by identifying the functional associations among the PTMs present in the protein. To do that, they combine five different evidence channels based on a literature survey, the modified residue co-evolution, their structural proximity, their competition for the same residue and the location within PTM highly-enriched protein regions (hotspots) and show the functional associations within the context of the protein architecture.

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Cite this (QuartetS-DB, RRID:SCR_011981)

URL: https://applications.bhsai.org/quartetsdb/

Resource Type: Resource, data or information resource, database

A large-scale orthology database for prokaryotes and eukaryotes inferred by evolutionary evidence. Contnet includes orthology predictions among 1621 complete genomes (1365 bacterial, 92 archaeal, and 164 eukaryotic), covering >7 million proteins and 4 million pairwise orthologs; Orthologous groups, comprising >300000 groups of orthologous proteins and >236000 corresponding gene trees; and inparalog groups, comprising >500000 groups of inparalogs.

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