Atlas

Atlas is a software package consisting of a collection of software tools to assemble whole-genome shotgun reads and combined shotgun reads and BAC reads. The Atlas package uses relational data models for each type of data. It incorporates local instances of GenBank, RefSeq, UniProt, Human Protein Reference Database (HPRD), Biomolecular Interaction Network Database (BIND), Online Mendelian Inheritance in Man (OMIM), Database of Interacting Proteins (DIP), Molecular Interactions Database (MINT), NCBI Taxonomy, IntAct, Gene Ontology (GO), LocusLink, Entrez Gene and HomoloGene.

Topic

Sequence assembly;Genomics;Whole genome sequencing

Detail

  • Operation: Sequence assembly;Genome assembly

  • Software interface: Command-line user interface

  • Language: C++, Java, Perl

  • License: Other

  • Cost: Free for non-commercial use

  • Version name: -

  • Credit: TX is supported by CIHR grant #MOP-53259, Juergen Kast and BFFO.

  • Input: -

  • Output: -

  • Contact: questions@bcm.edu, Sohrab P Shah sohrab@bioinformatics.ubc.ca, Yong Huang yongh@bioinformatics.ubc.ca, Tao Xu taoxu@bioinformatics.ubc.ca, Macaire MS Yuen mack@bioinformatics.ubc.ca, John Ling jling@bioinformatics.ubc.ca, BF Francis Ouellette francis@bioinformatics.ubc.ca

  • Collection: -

  • Maturity: Mature

Publications

  • Atlas - a data warehouse for integrative bioinformatics.
  • Shah SP, Huang Y, Xu T, Yuen MM, Ling J, Ouellette BF. Atlas - a data warehouse for integrative bioinformatics. BMC Bioinformatics. 2005 Feb 21;6:34. doi: 10.1186/1471-2105-6-34. PMID: 15723693; PMCID: PMC554782.
  • https://doi.org/10.1186/1471-2105-6-34
  • PMID: 15723693
  • PMC: PMC554782

Download and documentation

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