Launch prediction server Query precalculated results
Algorithms Prediction server Database query Output description Benchmark results

MuLDAS is a system for genotyping/subtyping viral sequences, based on a novel method that combines multidimensional scaling (MDS), also known as principal coordinate analysis (PCoA), and linear discriminant analysis (LDA). More on the mothodology ...

It has been applied to subtyping HIV-1 and genotyping HCV nucleotide and amino acid sequences, while its application to other viruses is in consideration. It is available as the following forms:

  • Web-based prediction server
    • For a given sequence in FASTA format, the extent of the viral genes are identified.
    • For each genic regions, MuLDAS assigns a genotype/subtype separately.
    • The output includes the predicted genotype/subtype with statistical significance and several downloadable files (multiple sequence alignment, distance matrix, and GGobi XML).
  • Database query of the precalculated genotype/subtype
    • The nucleotide and amino acid sequences of those viruses are periodically fetched from NCBI GenBank/GenPept.
    • Their genotypes/subtypes are predicted by the same method as employed by the prediction server.
    • The results are stored in a database and can be queried by primary accessions or GI numbers.
    • The output is also in the same format as the prediction server, but it includes the genotypes of HCV and subtypes of HIV-1 predicted by Los Alamos Nat'l Lab.
    • We are inquirying NCBI for the LinkOut service from their Entrez search results of 'nucleotide' and 'protein' databases.

MuLDAS was developed by the Bio-Data Mining Lab, Department of Bioinformatics and Life Sciences, Soongsil University, Seoul, Korea. Initial idea was conceived when we carried out the project funded by Korea Center for Disease Control (KCDC). The prototype was tested with HIV-1 nucleotide sequences by Yong Ju Ahn and presented in the poster session of ISBM2007, Vienna. The current version that was developed by Jiwoong Kim. Both of them were supported financially by the Brain Korea 21 "BT-IT Integrationist Program" of Korea Research Foundation (KRF) awarded to Dept. of Bioinformatics and Life Sciences, Soongsil University.

As it is intended to be a worldwide high-availability service with up-to-date underlying data, we have ported the system on a server operated by Korea Bioinformation Center (KOBIC). KOBIC is a national center operated by Korea Reserach Institute of Bioscience and Biotechnology (KRIBB) and funded by Korean Ministry of Education, Science and Technology (MEST, no English) through Korea Science and Engineering Foundation (KOSEF). MuLDAS is now serviced and maintained by KOBIC.

Copyrighted by Bio-Data Mining Lab, Department of Bioinformatics and Life Sciences, Soongsil University, Seoul, Korea