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Other Resources

Resources include databases, gene-collections, portals, and various tools related to the human genome.

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Found 28 links

Displaying 15 links

BEARRTool Content

http://giscompute.gis.a-star.edu.sg/~vega/BEARR1.0/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Human Genome > Other Resources
Model Organisms > Mouse and Rat

Batch Extraction and Analysis of cis-Regulatory Regions (BEARR) takes a list of gene identifiers (such as RefSeq and Unigene IDs), consensus patterns, and (optionally) a position weight matrix as input and returns a list of matches for the patterns in both the sense and anti-sense strands of the relevant genomic sequence. The user specifies what distance up and downstream from both the transcription start site and the 3\' terminus to look for the patterns.

NAR Web Server Issue 2004
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tagsbinding sites dna dna sequence analysis gene expression profiling nucleic acid regulatory sequences oligonucleotide array sequence analysis software design transcription factors

CREMETool Content

http://creme.dcode.org/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Other Resources

CREME (Cis-Regulatory Module Explorer for the human genome) is a tool for identifying and visualizing cis-regulatory modules for a given set of genes that are potentially co-expressed or co-regulated. It takes as input a list of accession numbers, and reports back common modules, grouping genes from the list by which modules are found in their promoter regions.

NAR Web Server Issue 2004
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tagsbinding sites computational biology gene expression regulation genetic promoter regions human genome humans transcription factors

DCODE.ORGResource Content

http://www.dcode.org/

Human Genome > Other Resources
Sequence Comparison > Comparative Genomics

The dcode.org website provides access to tools for comparative genomic analyses developed by the Comparative Genomics Center at the Lawerence Livermore National Laboratory. Tools include: zPicture, Mulan, eShadow, rVista, CREME, and the ECR Browser.

NAR Web Server Issue 2005
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tagsbase sequence binding sites computational biology gene expression regulation genetic promoter regions genomics humans molecular evolution nucleic acid regulatory sequences phylogeny sequence alignment transcription factors

Gene Set BuilderTool Content

http://www.cisreg.ca/gsb/

DNA > Sequence Retrieval and Submission
Human Genome > Annotations
Human Genome > Other Resources
Model Organisms > General Resources
Protein > Sequence Retrieval

Gene Set Builder is a database-driven, web-based tool designed to help researchers compile, store, export, and share sets of genes. This application supports the 17 eukaryotic genomes found in version 32 of the Ensembl database, which includes species from yeast to human. User-created information such as sets and customized annotations are stored and can be shared to facilitate easy access. Gene sets stored in the system can be exported in a variety of output formats - as lists of identifiers, in tables, or as sequences.

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tagscomputational biology database management systems factual databases fungal genes gene expression regulation genetic databases genome genomics humans programming languages

GeneHub-GEPISTool Content

http://www.cgl.ucsf.edu/Research/genentech/genehub-gepis/

Expression > cDNA, EST, SAGE
Human Genome > Other Resources
Model Organisms > Mouse and Rat

GeneHub-GEPIS is a tool for inferring human and mouse gene expression patterns based on normalized EST abundance in various normal and cancerous tissues.

NAR Web Server Issue 2007
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tagsalgorithms biological tumor markers chromosome mapping dna sequence analysis expressed sequence tags gene expression profiling genetic testing humans neoplasms online systems sequence alignment

Genome Centres and DatabasesResource Content

http://www.ncbi.nlm.nih.gov/genomes/static/links.html

DNA > Mapping and Assembly
Human Genome > Other Resources
Model Organisms > General Resources

Genome centers and databases listed by organism.

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GenomeNetTool Content

http://www.genome.ad.jp/

DNA > Sequence Retrieval and Submission
Human Genome > Other Resources
Protein > Interactions, Pathways, Enzymes
Protein > Sequence Retrieval

Network of database and computational resources including KEGG (pathways, interactions, etc.) and DBGET/LinkDB (an integrated database retrieval system). It also hosts several web-based tools for sequence analysis (ie. Blast, Motif, Clustal W)

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tagsamino acid sequence animals biological models computer simulation factual databases genetic models genome humans information systems japan ligands molecular biology molecular sequence data protein binding proteome

HGNC: HUGO Gene Nomenclature CommitteeResource Content

http://www.genenames.org

DNA > DNA and Genomic Analysis
DNA > Sequence Retrieval and Submission
Human Genome > Other Resources
Protein > Sequence Retrieval

The HGNC approves a unique gene name and symbol for each known human gene. The HGNC Database is searchable and contains all approved symbols. For each symbol, if known, the database associates gene location, aliases, previous symbols and links out to sequence data and other databases.

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tagsanimals computational biology genes genetic databases genetic variation genomics human genome humans mice systems integration terminology as topic

HMDBDatabase Content

http://www.hmdb.ca/

Human Genome > Other Resources
Other Molecules > Metabolites

The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body. The database supports extensive text, sequence, chemical structure and relational query searches.

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tagsbiochemical phenomena biochemistry biomolecular nuclear magnetic resonance humans metabolism organ transplantation

Human Ageing Genomic ResourcesResource Content

http://genomics.senescence.info/index.html

Computer Related > Bio-* Programming Tools
Human Genome > Other Resources

The Human Ageing Genomic Resources (HAGR) website provides tools and curated databases relevant to the genetics of human ageing. GenAge is a database of genes related to human ageing, and AnAge is a multi-species database facilitating the comparative biology of ageing. The Ageing Research Computational Tools (ARCT) is a collection of Perl modules to assist comparative genomics research.

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Human Genome Variation NomenclatureResource Content

http://www.hgvs.org/rec.html

Human Genome > Annotations
Human Genome > Genomics
Human Genome > Other Resources
Human Genome > Sequence Polymorphisms

The Human Genome Society has established a committee to suggest standards for the description of sequence variants in DNA, RNA, and protein sequences. The standards are linked here.

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IDconverterTool Content

http://idconverter.bioinfo.cnio.es/IDconverter.php

Expression > Transcript Expression Analysis
Human Genome > Other Resources

IDconverter is a tool that converts gene, clone or protein IDs to other IDs which can be especially useful for microarray data analyses. This application is part of the suite Asterias.

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IdiographicaTool Content

http://www.ncrna.org/idiographica/

DNA > DNA and Genomic Analysis
Human Genome > Other Resources
Model Organisms > Mouse and Rat

Idiographica is a general-purpose web application to build idiograms on-demand for human, mouse and rat. It allows users to generate high-quality idiograms with custom annotation according to their own genome-wide mapping/annotation data through an easy-to-use interface.

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tagsalgorithms animals chromosome banding chromosome mapping humans mice rats

Intergr8Tool Content

http://www.ebi.ac.uk/integr8/

Human Genome > Other Resources
Model Organisms > General Resources

Integr8 is a browser for information relating to completed genomes and proteomes. It provides access to species descriptions, literature, statistical analysis and summary information about each complete proteome; and integrates data from a variety of sources, including InterPro, CluSTr and GO.

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tagsarchaeal dna bacterial dna genetic databases genomics proteomics systems integration

LIPID MAPSTool Content

http://www.lipidmaps.org/tools/index.html

Human Genome > Other Resources
Other Molecules > Metabolites

LIPID Metabolites And Pathways Strategy (LIPID MAPS) is a consortium that presents a collection of tools for performing tasks such as drawing lipid structures and predicting possible structures from mass spectrometry data.

NAR Web Server Issue 2007
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tagsanimals chemical models computational biology database management systems factual databases glycosphingolipids humans isomerism lipid metabolism lipids mice molecular conformation molecular structure polysaccharides protein databases proteome proteomics terminology as topic

Tags associated with subcategory 'Human Genome/Other Resources'

humans animals computational biology mice genomics human genome algorithms base sequence gene expression regulation dna sequence analysis binding sites factual databases sequence alignment cluster analysis chromosome mapping conserved sequence transcriptional regulatory elements genetic promoter regions genetic transcription statistical models t-lymphocyte epitopes major histocompatibility complex least-squares analysis dna fingerprinting sensitivity and specificity single nucleotide polymorphism molecular models multivariate analysis quantitative structure-activity relationship protein sequence analysis protein databases online systems peptides hla antigens genetic polymorphism proteome protein binding molecular biology japan ligands database management systems dna nucleic acid sequence homology molecular sequence data human genome project expressed sequence tags genes information systems genome nucleic acid databases National Center for Biotechnology Information (NCBI) kir receptors temperature immunologic receptors gene expression profiling nucleic acid regulatory sequences genetic models computer simulation transcription factors oligonucleotide array sequence analysis software design predictive value of tests polymerase chain reaction dna-binding proteins organ transplantation metabolism biochemistry biomolecular nuclear magnetic resonance neoplasm antigens proteins national institutes of health (u.s.) mammals gene library type ii dna topoisomerases complementary dna biochemical phenomena mutation forecasting antigen presentation bacterial dna dna mutational analysis archaeal dna hla-a antigens chemical models alleles pubmed hla-dr antigens hla-b antigens dna primers artificial intelligence open reading frames private sector biological tumor markers terminology as topic proteomics molecular structure polysaccharides genetic testing neoplasms histocompatibility antigens class i species specificity