PlatCom: A Platform for Computational Comparative Genomics


PlatCom (A Platform for Computational Comparative Genomics) is a system for the comparative analysis of multiple organisms. It consists of three components: databases of biological entities; databases of relationships among entities; and a suite of mining applications over the databases. Computing relationships between biological entities and mining the database present a computational challenge that we intend to solve using two approaches. The first solution involves simply exploiting the high performance computing power at Indiana -- AVIDD Linux and IBM SP clusters. The second approach focuses on the development of novel efficient data mining algorithms on top of existing efficient algorithmic libraries, including LEDA and boost graph libraries (www.boost.org).

Try PLATCOM platcom.org
References
Most of algorithms and systems we have been developing is used for PLATCOM. See the publication page for Sun Kim.

One unique feature of PLATCOM is use of high performance data mining tools (in-house or those in the public domain). Thus algorithm development is an essential part of PLATCOM. Check
  • BAG: A Graph Theoretic Sequence Clustering Algorithm
  • GAME and a mutliple genome alignment algorithm using BAG
  • Mining Correlated Gene Sets in Multiple Genomes
  • Motif discovery framework


    • In addition, several specialized systems are being built upon PLATCOM:
  • CGAS, A comparative genome annotation system
  • ComPath, A pathway analysis system, and
  • CLASSEQ, A genome-level sequence clustering system


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