Center for Biological Language Modeling

 

Biological Language Modeling Toolkit (BLMT) is a collection of programs that aid in statistical analysis of Genome sequences. This toolkit is explained at a greater length in "Comparative n-gram analysis of whole-genome Protein Sequences", presented at HLT2002 [1].

A brief note on installing this package is found in Readme.txt.
[This page is still being updated. Please check back or write to us if you have specific questions.]

Source Code
Version 1 Mar-2002.
Version 1.5 Feb-2003.
(Some minor corrections have been made so that the code compiles on Solaris. If you find any issues or discrepencies in the code, please write to us.)

Developed by
Madhavi K. Ganapathiraju
Judith Klein-Seetharaman

Publications

  1. "Collaborative Discovery and Biological Language Modeling Interface",
    Madhavi Ganapathiraju, Vijayalaxmi Manoharan, Raj Reddy and Judith Klein-Seetharaman,
    Lecture Notes in Artificial Intelligence LNCS/LNAI 3864, 2006.
  2. "BLMT: Statistical sequence analysis using n-grams",
    Madhavi Ganapathiraju, Vijayalaxmi Manoharan and Judith Klein-Seetharaman,
    Applied Bioinformatics,vol. 3, issue 2, November 2004.
  3. "Computational Biology and Language",
    Madhavi Ganapathiraju, N. Balakrishnan, Raj Reddy and Judith Klein-Seetharaman,
    Lecture Notes in Artificial Intelligence, LNCS/LNAI 3345, 2004.
  4. "Comparative n-gram analysis of whole-genome sequences",
    Madhavi Ganapathiraju, Judith Klein-Seetharaman, Roni Rosenfeld, Jaime Carbonell and Raj Reddy,  
    HLT'02: Human Language Technologies Conference, San Diego, March, 2002.
  5. "Rare and frequent amino acid n-grams in whole-genome protein sequences", (poster) 
    Madhavi Ganapathiraju, Judith Klein-Seetharaman, Roni Rosenfeld, Jaime Carbonell and Raj Reddy,  
    RECOMB'02: The Sixth Annual International Conference on Research in Computational Molecular Biology, Washington DC, USA, April, 2002.
  6. "Comparative n-gram analysis of genome sequences", (poster) 
    Madhavi Ganapathraju, Judith Klein-Seetharaman, Jaime Carbonell, Roni Rosenfeld and Raj Reddy,  
    Proc. International Symposium On Crystallography And Bioinformatics in Structural Biology, Bangalore, India, November, 2001. 
  7. "Differences in usage of local combinations of amino acids in various genomes",   (poster)
    Judith Klein-Seetharaman, Madhavi Ganapathiraju, Jaime Carbonell, Roni Rosenfeld and Raj Reddy,  
    Proc. International Symposium On Crystallography And Bioinformatics in Structural Biology, Bangalore, India, November, 2001.


write-to: madhavi@cs.cmu.edu   Web Page created Mar, 2002, Updated June, 2003.