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eSLDB - Eukaryotic Subcellular Localization Database

eSLDB - Eukaryotic Subcellular Localization Database | bioinformatics-databases | Scoop.it

eSLDB is a database of protein subcellular localization annotation for eukaryotic organisms. It contains experimental annotations derived from primary protein databases, homology based annotations and computational predictions.

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Kidhome - The Kidney Development Database

Kidhome - The Kidney Development Database | bioinformatics-databases | Scoop.it
Reading Material
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GOBASE - The Organelle Genome Database

GOBASE - The Organelle Genome Database | bioinformatics-databases | Scoop.it

GOBASE is a taxonomically broad organelle genome database that organizes and integrates diverse data related to mitochondria and chloroplasts. GOBASE is currently expanding to include information on representative bacteria that are thought to be specifically related to the bacterial ancestors of mitochondria and chloroplasts.


The current version of GOBASE, release 25, is based on GenBank release 175 and was released in June 2010. This release includes 177,000 new mitochondrial sequences and 41,000 new chloroplast sequences.

Unfortunately, funding for GOBASE has expired, so this will be the last update. Maintenance of GOBASE will cease at the end of August 2010 and the contact address gobase@bch.umontreal.ca will also become defunct at this time.


Users are requested to cite GOBASE in any publication making use of GOBASE data. The preferred reference is:

GOBASE - an organelle genome database

O'Brien, Emmet A., Zhang, Yue, Wang, Eric, Marie, Veronique, Badejoko, Wole, Lang, B. Franz and Burger, Gertraud.
Nucleic Acids Res. 37:D946-950 (2009)


Full text available here


[ OGMP | FMGP | GOBASE | PID | CIAR-PEB | ISEP | Entrez | Blast | Analysis | Resources | Organelle genomes ]

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dbERGE II - a database of experimental results on gene expression

dbERGE II - a database of experimental results on gene expression | bioinformatics-databases | Scoop.it

dbERGE II stores experiment and result details for various types of experiments. The current types of experiments available are:

  1. DNA transfer experiments (Transfections and Transgenic mice) 
  2. Binding assays (Gel shift, In-vivo footprint, In-vitro footprint and Methylation interference) 
  3. Hypersensitive sites 
  4. ChIP - on - chip experiments

Explanation of each experiment type is given here.


Help and Documentation
Instructions for query page
Key for the query page's graphical display
Database schema diagrams
Frequently asked questions
How to contact us


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GiardiaDB : The Giardia genome resource

GiardiaDB : The Giardia genome resource | bioinformatics-databases | Scoop.it





GiardiaDB annotation will be updated based on expert community annotation provided by you. More details available by following this link.

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GermSAGE - a male germ cell transcriptome database

GermSAGE - a male germ cell transcriptome database | bioinformatics-databases | Scoop.it

GermSAGE is a collection of male germ cell transcriptiome information derived from Serial Analysis of Gene Expression (SAGE). It includes the three key germ cell stages in spermatogenesis, including mouse type A spermatogonia (Spga), pachytene spermatocytes (Spcy), and round spermatids (Sptd). A total of 452,095 SAGE tags are represented in all the libraries and is by far the most comprehensive resource available.


Genome view of complete data set

A global view of germ cell transcriptome data in the UCSC Genome browser.


Full text or specific field search

Search genes or specify searching criteria based on tag sequence, chromosomal location or tag counts.


Section on Developmental Genomics: http://scg.nichd.nih.gov

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GenProtEC – an updated and improved analysis of functions of Escherichia coli K-12 proteins

GenProtEC – an updated and improved analysis of functions of Escherichia coli K-12 proteins | bioinformatics-databases | Scoop.it

Using more than one approach to characterizing functions of unknown proteins, we now present in GenProtEC (http://genprotec.mbl.edu/) some level of function information for 87% of Escherichia coli K-12 proteins. A new approach that has yielded new information entails assigning content of structural domains and their functions to E.coli proteins. In addition, some earlier methods have been further refined to provide more meaningful data. The process of identifying and separating multimodular or fused proteins into component modules has been improved. As a result, groups of sequence-similar (paralogous) proteins have been refined. Experimental information from recent literature on previously unknown genes has been incorporated. We now use a rich system of characterizing cell roles which accents the fact that many proteins play more than one cellular role and therefore carry more than one designation from our detailed catalog of roles, MultiFun.


Gene/Protein Query
Search by Gene Name, B-number, ECK Number, Swiss-Prot Accession Number and ID, Enzyme Nomenclature (E.C. number), Protein Name, Gene Type, or Physiological Role.


Overview of E. coli genome by Gene Type distribution

Protein Modules
A list of fused E. coli proteins separated into modular units.


Protein Groups
Sequence related groups of E. coli proteins. 
Structurally and biochemically related groups of E. coli proteins.


MultiFun Classification System
MultiFun a classification system for cellular/physiological roles of gene products.
MultiFun2GO conversion of Multifun to Gene Ontology terms.


SCOP superfamily assignments to E. coli proteins
SCOP superfamily distribution.
SCOP assignments.


Downloadable Tables


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HAGR – Human Ageing Genomic Resources

HAGR – Human Ageing Genomic Resources | bioinformatics-databases | Scoop.it
The Human Ageing Genomic Resources (HAGR) is a collection of databases and tools designed to help researchers study the genetics of human ageing using modern approaches such as functional genomics, network analyses, systems biology and evolutionary analyses.


GenAge

A major resource in HAGR is GenAge, which includes a curated database of genes related to human ageing and a database of ageing- and longevity-associated genes in model organisms

 Search human genes
 Search model organism genes

AnAge

Another major database in HAGR is AnAge. Featuring over 4,000 species, AnAge provides a compilation of data on ageing, longevity, and life history that is ideal for the comparative biology of ageing.


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GenomeTraFaC - a database for putative cis-regulatory regions of RefSeq Gene Orthologs

GenomeTraFaC - a database for putative cis-regulatory regions of RefSeq Gene Orthologs | bioinformatics-databases | Scoop.it

A comparative genomics-based resource for initial characterization of gene models and the identification of putative cis-regulatory regions of RefSeq Gene Orthologs.

 Find conserved cis-element clusters within BlastZ-identified conserved sequence alignment blocks.

 Find shared cis-elements between user-selected gene segment pairs.

 Genome-wide ortholog conserved Cis-element module search

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HGT-DB - a database of putative horizontally transferred genes in prokaryotic complete genomes

HGT-DB - a database of putative horizontally transferred genes in prokaryotic complete genomes | bioinformatics-databases | Scoop.it

The Horizontal Gene Transfer DataBase (HGT-DB) is a genomic database that includes statistical parameters such as G+C content, codon and amino-acid usage, as well as information about which genes deviate in these parameters for prokaryotic complete genomes. Under the hypothesis that genes from distantly related species have different nucleotide compositions, these deviated genes may have been acquired by horizontal gene transfer. The current version of the database contains 88 bacterial and archaeal complete genomes, including multiple chromosomes and strains. For each genome, the database provides statistical parameters for all the genes, as well as averages and standard deviations of G+C content, codon usage, relative synonymous codon usage and amino-acid content. It also provides information about correspondence analyses of the codon usage, plus lists of extraneous group of genes in terms of G+C content and lists of putatively acquired genes. With this information, researchers can explore the G+C content and codon usage of a gene when they find incongruities in sequence-based phylogenetic trees. A search engine that allows searches for gene names or keywords for a specific organism is also available. HGT-DB is freely accessible at http://www.fut.es/~debb/HGT

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GenomeRNAi - a database for RNAi phenotypes and reagents

GenomeRNAi - a database for RNAi phenotypes and reagents | bioinformatics-databases | Scoop.it
GenomeRNAi features 168 RNAi screens in human, and 181 screens in drosophila, as well as a NEW functionality - overlay genes sharing the same phenotype onto networks in StringDB. GenomeRNAi is recommended data repositoryby Nature’s new “Scientific Data“ publication format. Looking forward to your RNAi data submissions! Europe PMC provides links to GenomeRNAi - check out the current list.
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Mapper - a Multi-Genome Analysis of Positions and Patterns of Elements of Regulation Database

Mapper - a Multi-Genome Analysis of Positions and Patterns of Elements of Regulation Database | bioinformatics-databases | Scoop.it

The MAPPER Database contains putative Transcription Factor Binding Sites (TFBSs) located in the upstream sequences of genes from the human, mouse and D.melanogaster genomes. For each transcript, the region scanned extends from 10,000bp upstream of the transcript start to 50bp downstream of the coding sequence start. Therefore, the database contains putative binding sites in the gene promoter and in the initial introns and non-coding exons.

 

Information displayed for each putative binding site includes the transcription factor name, its position (absolute on the chromosome, or relative to the gene), the score of the prediction, and the region of the gene the site belongs to. If the selected gene has homologs in any of the other two organisms, the program optionally displays the putative TFBSs in the homologs.


The MAPPER Database is part of the MAPPER platform, that also includes the MAPPER Search Engine, and rSNPs. Please go the the MAPPER main page to access the other MAPPER modules.


If you use this program for your research please cite:

Marinescu, V. D., Kohane, I. S., and Riva, A. (2005). The MAPPER database: a multi-genome catalog of putative transcription factor binding sitesNucleic Acids Res33 (Database Issue), D91-97.

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ENCODE Project at UCSC - Encyclopedia of DNA Elements

ENCODE Project at UCSC - Encyclopedia of DNA Elements | bioinformatics-databases | Scoop.it

The Encyclopedia of DNA Elements (ENCODE) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active.


ENCODE data are now available for the entire human genome. 


All ENCODE data are free and available for immediate use via :



To search for ENCODE data related to your area of interest and set up a browser view, use the UCSC Experiment Matrix or Track Search tool (Advanced features). The Experiment List (Human) and Experiment List (Mouse) links provide comprehensive listings of ENCODE data that is released or in preparation.


All ENCODE data is freely available for download and analysis. However, before publishing research that uses ENCODE data, please read the ENCODE Data Release Policy, which places some restrictions on publication use of data for nine months following data release.    


Read more about ENCODE data at UCSC.

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RAD - Rice Annotation Database

RAD - Rice Annotation Database | bioinformatics-databases | Scoop.it

RAD is a contig-oriented database for high-quality manual annotation of RGP, which can present non-redundant contig analyses by merging the accumulated PAC/BAC clones.


As of October 2004, the database contains a total of 215 Mb sequence with relevant annotation results (30000 predicted genes.) The database can provide the latest information on manual annotation as well as a comprehensive structural analysis of various features of the rice genome.


Note that the annotation data of chromosomes 1, 3, 4 and 10 are restored from flat files of the public database. These basically contain the predicted genes information but not contain their evidence information.

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GOLD.db: genomics of lipid-associated disorders database

GOLD.db: genomics of lipid-associated disorders database | bioinformatics-databases | Scoop.it


The GOLD.db (Genomics of Lipid-Associated Disorders Database) was developed to address the need for integrating disparate information on the function and properties of genes and their products that are particularly relevant to the biology, diagnosis management, treatment, and prevention of lipid-associated disorders.


Journals * Glossary Meetings * Search Institutions

Database Model Bioinformatics * Microarrays * Databases * Tools

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HbVar - A Database of Human Hemoglobin Variants and Thalassemias

HbVar - A Database of Human Hemoglobin Variants and Thalassemias | bioinformatics-databases | Scoop.it

This is a relational database of information about hemoglobin variants and mutations that cause thalassemia. The initial data came from Syllabi authored by Prof. Titus H.J. Huisman, Mrs. Marianne F.H. Carver, Dr. Erol Baysal, and Prof. Georgi D. Efremov. This information was converted to a database, and now new entries are added and old entries are corrected by our curators, Dr. Henri Wajcman, Dr. George Patrinos, Dr. Kamran Moradkhani, Joseph Borg, and Philippe Joly. HbVar results from a collaboration among several investigators at Penn State University (USA), INSERM Creteil (France), and Boston University Medical Center (USA). Visit our query page or summary page to see the types of information available.

To query on the database, click here.


To access summaries of the categories of the mutations, click here. 
Summaries of mutation categories has counts of the results for common queries and buttons to link to them. 

Most recent update
Difference in mass chart
XPRbase has experimental protocols
FINDbase-related links
    Search FINDbase for beta allele frequencies
    Search FINDbase for alpha allele frequencies
    Search FINDbase for delta allele frequencies
    Note: You may have to install Silverlight software to view the FINDbase pages.
Help Page 
    Help with numbers 
    Help with HGVS nomenclature 
Frequently Asked Questions

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snp :: topoSNP Database

snp :: topoSNP Database | bioinformatics-databases | Scoop.it

Welcome to the topoSNP database. This site produces an interactive visualization of disease and non-disease associated non-synonymous single nucleotide polymorphisms (nsSNPs) and displays geometric and relative entropy calculations.


*** Please note you will need MDL's Chime Plugin to view this page correctly. It can be freely downloaded at http://www.mdlchime.com.***


To start, please select one of the datasets to the right, or enter a protein sequence to BLAST search our database.


Relevant publication TopoSNP, Nucleic Acids Research, 2004

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Genetics Home Reference - Your guide to understanding genetic conditions

Genetics Home Reference - Your guide to understanding genetic conditions | bioinformatics-databases | Scoop.it
Genetics Home Reference (GHR) provides free access to consumer-friendly information on medical genetics to patients and their family members, health care professionals, and the public. The site offers summaries for a broad range of inherited conditions or disorders caused by gene alterations. Each condition summary includes the causes, available genetic testing, and links to summaries on related genes. Descriptions of genes include gene names and their synonyms, normal function, chromosome location, and an explanation of any disorder-causing mutations. Additionally, GHR provides a genetics glossary, help on understanding genetics, and links to many useful consumer, support, and research organizations. GHR is a service of the U.S. National Library of Medicine at the National Institutes of Health.


How can I find a genetics professional in my area?


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Comparative Genomics Group

Comparative Genomics Group | bioinformatics-databases | Scoop.it

Comparative Genomics Group belongs to the MRC Functional Genomics Unit at the Department of Physiology, Anatomy and Genetics of the University of Oxford. Please see our portal pages for more information.


OPTIC Orthologous and Paralogous Transcripts in Clades.

We have looked at complete genomes in several clades. You can browse and download the results for Flies (12 species) - Nematodes (4 species) - Amniota (6 species: human, dog, mouse, monodelphis, platypus, chicken) - Yeasts (7 species) - Vertebrates (8 species) - Grape


Pairwise probabilistic alignments.

Gene predictions Gene predictions by homoloy based on Guy Slater's exonerate. Gene predictions are available for browsing and download.

Flies: Gene predictions in Drosophila species as part of the AAA Project.


Also available for download are multiple alignments, orthologogy assignments used in Heger, A. and Ponting, CP.. (2007). Evolutionary rate analyses of orthologs and paralogs from 12 drosophila genomes. Genome Res 17:1837-1849.


Mammals: Gene predictions in Opossum (Monodelphis domestica) and Platypus (Ornithorhynchus anatinus).CodonbiasSupplementary material to: Heger & Ponting (2007) Variable strength of translational selection among 12 Drosophila species. Genetics. Nov;177(3):1337-48

A Transcriptomic Atlas of Mouse Neocortical Layers 

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OrysPSSP: a curated database for small secreted proteins from rice

OrysPSSP: a curated database for small secreted proteins from rice | bioinformatics-databases | Scoop.it

Oryza sativa (ssp. japonica), as one of the most important food crops, was among the first to be sequenced, greatly facilitating genetic and physiological research in agriculture and plant biology. However, annotation of genes in the short-length range was proved inadequate to many plant genomes in general, especially for small secreted peptides found to be involved in diverse physiological processes, i.e. stress response, flowering, hormone signaling, etc. Studies showed that the numbers of small secreted proteins were underestimated. As both an economic crop and a model plant, it is a top priority for us to address this issue in rice (Oryza sativa ssp. japonica). 


    We made an effort to provide plant biologists a comprehensive comparative platform: OrysPSSP. It provides the data of small secreted proteins, 25-250 aa, on a genome-scale, integrated with a variety of search tools, validation functions and comparative resources. The current official release (v0530) contains a wholly set of 101,048 candidates. About two-thirds of them, 67,559, are located in un-annotated genome regions, while the rest, 33,489, are included in known genes. For each candidate, users are provided with chromosomal location, peptide sequence and domain(s), organelle location, gene annotation and neighboring genes. Validated with different data sets, 33,350 proteins were supported by tiling Array data, 9,431 by RNAseq data, and 18,353 by mass spectrum results. When comparing across the phylogeny of 25 green plants, we found the number of conserved SSPs between rice and other plants, in general, was inversely proportional to their evolutionary distance. 


    On top of the curated data for small secreted proteins from rice, we developed a number of tools to help rice scientists and plant biologists in obtaining (sub)datasets that are relevant and valuable to their fields of studies. Users can view the distribution of small secreted proteins on rice chromosomes, and browse the data by chromosome. Alternatively, they can search for small secreted protein genes and retrieve data by applying one or more filter parameters, i.e. gene keyword, domain name, chromosome location, annotation status, etc. A "BLAST" tool is also provided to seek small secreted proteins mapped to users' query sequences. Query sequence can be chose from three different types, genomic sequence (DNA), mRNA sequence (mRNA), or protein sequence (Protein). In our testing releases, the most important function users found, is the validation tool supported by our database. Currently we offered three separate datatypes, tilingArray, transcriptomics and proteomics, (all from public available data sources) to validate and filter small secreted protein candidates. A comparative genomics tool for a comprehensive analysis of the conservation of SSPs in 26 green plants was build. We integrated the genome information from 25 plant species besides Oryza sativa ssp. japonica. Comparison across the phylogeny would yield insight into the occurrence and evolution of SSPs in green plants. 


USEFUL LINKS:

The Rice Annotation Project: Nipponbare genome sequencing by the International Rice Genome Sequencing Project. 

Rice Expression Profile DatabaseRepository of gene expression data in rice.

Flowering Plant Gene Picker: Annotation pipeline for flowering plant genomes.

Phytozome v8.0:Comparative genomic amongst green plants.

Arabidopsis Unannotated Secreted Peptide Database:Predictions of putative unannotated secreted peptides from Arabidopsis thaliana.

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BCBC Genomics - Beta Cell Biology Database

BCBC Genomics - Beta Cell Biology Database | bioinformatics-databases | Scoop.it

BCBC Genomics provides searches and tools to explore detailed information about genes, transcripts, gene interactions, genomic regions, and functional genomics studies.

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Bioinformatics Educational Sites

Bioinformatics Educational Sites | bioinformatics-databases | Scoop.it




  1. The Bioinformatic Resource (CCP11) 
  2. Pedro's BioMolecular Research 
  3. Bioinformatics and Genomics Resources 
  4. BCM - Search Launcher 
  5. Sequence Analysis Tools (NIH) 
  6. Biology WorkBench (SDSC) 
  7. EBI 
  8. NCBI 
  9. Pacific Symposium on Biocomputing - Proceedings 
  10. The International Society for Computational Biology 
  11. bioinformatik.de 
  12. ExPASy 
  13. The USC Sequence Alignment Server 
  14. BioNetbook 
  15. BMERC 
  16. Atelier BioInformartique (aBi) 
  17. Amos' links 
  18. Genamics SoftwareSeek 
  19. CMS Molecular Biology Resource 
  20. Bioplanet

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HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection

HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection | bioinformatics-databases | Scoop.it

The highly expressed genes database (HEG-DB) is a genomic database that includes the prediction of which genes are highly expressed in prokaryotic complete genomes under strong translational selection. The current version of the database contains general features for almost 200 genomes under translational selection, including the correspondence analysis of the relative synonymous codon usage for all genes, and the analysis of their highly expressed genes. For each genome, the database contains functional and positional information about the predicted group of highly expressed genes. This information can also be accessed using a search engine. Among other statistical parameters, the database also provides the Codon Adaptation Index (CAI) for all of the genes using the codon usage of the highly expressed genes as a reference set. The 'Pathway Tools Omics Viewer' from the BioCyc database enables the metabolic capabilities of each genome to be explored, particularly those related to the group of highly expressed genes. The HEG-DB is freely available at http://genomes.urv.cat/HEG-DB.


EGG's HOME


DATABASES

HGT-DB

HEG-DB



APLICATIONS

OPTIMIZER

TOPD/FMTS

RCDI

E-CAI

CAIcal

D-UPGMA

Translate

ORF-Search 


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PReMod: a database of genome-wide mammalian cis-regulatory module predictions

PReMod: a database of genome-wide mammalian cis-regulatory module predictions | bioinformatics-databases | Scoop.it

PReMod, a new database of genome-wide cis-regulatory module (CRM) predictions for both the human and the mouse genomes. The prediction algorithm, described previously in Blanchette et al. (2006) Genome Res.16, 656–668, exploits the fact that many known CRMs are made of clusters of phylogenetically conserved and repeated transcription factors (TF) binding sites. Contrary to other existing databases, PReMod is not restricted to modules located proximal to genes, but in fact mostly contains distal predicted CRMs (pCRMs). Through its web interface, PReMod allows users to (i) identify pCRMs around a gene of interest; (ii) identify pCRMs that have binding sites for a given TF (or a set of TFs) or (iii) download the entire dataset for local analyses. Queries can also be refined by filtering for specific chromosomal regions, for specific regions relative to genes or for the presence of CpG islands. The output includes information about the binding sites predicted within the selected pCRMs, and a graphical display of their distribution within the pCRMs. It also provides a visual depiction of the chromosomal context of the selected pCRMs in terms of neighboring pCRMs and genes, all of which are linked to the UCSC Genome Browser and the NCBI.


PReMod: http://genomequebec.mcgill.ca/PReMod.

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Mapper - a Multi-Genome Analysis of Positions and Patterns of Elements of Regulation Database

Mapper - a Multi-Genome Analysis of Positions and Patterns of Elements of Regulation Database | bioinformatics-databases | Scoop.it

The MAPPER Database contains putative Transcription Factor Binding Sites (TFBSs) located in the upstream sequences of genes from the human, mouse and D.melanogaster genomes. For each transcript, the region scanned extends from 10,000bp upstream of the transcript start to 50bp downstream of the coding sequence start. Therefore, the database contains putative binding sites in the gene promoter and in the initial introns and non-coding exons.

 

Information displayed for each putative binding site includes the transcription factor name, its position (absolute on the chromosome, or relative to the gene), the score of the prediction, and the region of the gene the site belongs to. If the selected gene has homologs in any of the other two organisms, the program optionally displays the putative TFBSs in the homologs.


The MAPPER Database is part of the MAPPER platform, that also includes the MAPPER Search Engine, and rSNPs. Please go the the MAPPER main page to access the other MAPPER modules.


If you use this program for your research please cite:

Marinescu, V. D., Kohane, I. S., and Riva, A. (2005). The MAPPER database: a multi-genome catalog of putative transcription factor binding sitesNucleic Acids Res33 (Database Issue), D91-97.

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