Genome data mining for everyone.

The genomic sequences of a huge number of species have been determined. Typically, these genome sequences and the associated annotation data are accessed through Internet-based genome browsers that offer a user-friendly interface. Intelligent use of the data should expedite biological knowledge discovery. Such activity is collectively called data mining and involves queries that can be simple, complex, and even combinational. Various tools have been developed to make genome data mining available to computational and experimental biologists alike. In this mini-review, some tools that have proven successful will be introduced along with examples taken from published reports.

• Publication year

  2008

• Venue

  BMB Reports

• Publication date

  2008-11-30

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.5483/BMBREP.2008.41.11.757PMID 19017486
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes

  2008cited by this paper
• OGtree: a tool for creating genome trees of prokaryotes based on overlapping genes

  2008cited by this paper
• Gene expression module-based chemical function similarity search

  2008cited by this paper
• The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata

  2008cited by this paper
• The complete genome of an individual by massively parallel DNA sequencing

  2008cited by this paper
• Mapping and sequencing of structural variation from eight human genomes

  2008cited by this paper
• Next-generation sequencing: the race is on.

  2008cited by this paper
• Advanced Genomic Data Mining

  2008cited by this paper
• Automated Querying of Genome Databases

  2007cited by this paper
• The Diploid Genome Sequence of an Individual Human

  2007cited by this paper
• Ensembl 2008

  2007cited by this paper
• Bioinformatics and Computational Biology Solutions Using R and Bioconductor

  2007cited by this paper
• A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly.

  2007cited by this paper
• Database resources of the National Center for Biotechnology Information

  2007cited by this paper
• ARED Organism: expansion of ARED reveals AU-rich element cluster variations between human and mouse

  2007cited by this paper
• The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata

  2007cited by this paper
• Nucleic Acids Research, 2007, 1–6

  2007cited by this paper
• The UCSC Genome Browser Database: 2008 update

  2007cited by this paper
• CONSTRUCTING THE TREEFAM DATABASE

  2006cited by this paper
• Anticipating the $1,000 genome

  2006cited by this paper
• The ENCODE Project at UC Santa Cruz

  2006cited by this paper
• Discovery of regulatory elements in vertebrates through comparative genomics

  2005cited by this paper
• BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis

  2005cited by this paper
• Galaxy: a platform for interactive large-scale genome analysis.

  2005cited by this paper
• An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing.

  2005cited by this paper
• Exploring relationships and mining data with the UCSC Gene Sorter.

  2005influential reference
• Bioinformatics in the post-genome era.

  2004cited by this paper
• Finishing the euchromatic sequence of the human genome

  2004cited by this paper
• An overview of Ensembl.

  2004cited by this paper
• The UCSC Table Browser data retrieval tool

  2004cited by this paper
• Finishing the euchromatic sequence of the human genome

  2004cited by this paper
• The ENCODE (ENCyclopedia Of DNA Elements) Project

  2004cited by this paper
• To order or request additional

  2004cited by this paper
• A gene atlas of the mouse and human protein-encoding transcriptomes.

  2004cited by this paper
• EnsMart: a generic system for fast and flexible access to biological data.

  2003influential reference
• Human-mouse alignments with BLASTZ.

  2003cited by this paper
• The UCSC Genome Browser Database

  2003cited by this paper
• BLAT--the BLAST-like alignment tool.

  2002cited by this paper
• Under construction: building a safer industry.

  2002cited by this paper
• A user's guide to the human genome

  2002cited by this paper
• The human genome browser at UCSC.

  2002cited by this paper
• The sequence of the human genome (abstract only)

  2001cited by this paper
• Initial sequencing and analysis of the human genome

  2001cited by this paper
• The genome sequence of Drosophila melanogaster.

  2000cited by this paper
• Genome sequence of the nematode C. elegans: a platform for investigating biology.

  1998cited by this paper
• Life with 6000 Genes

  1996cited by this paper
• Sequence the Human Genome

  1986cited by this paper
• Nucleotide sequence of bacteriophage φX174 DNA

  1977cited by this paper
• Nucleotide sequence of bacteriophage phi X174 DNA.

  1977cited by this paper

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• A Grid based Mining Approach to Genomic Data Set

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• Discovery: Computational Systems Biology (CSB) in Health and Disease I

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