Centre Robert-Cedergren
    Bioinformatics & Genomics     2900 Edouard-Montpetit
    Montréal, Québec  H3T 1J4
    Canada
   

 

Amy M. Hauth

amy.hauth@umontreal.ca

      Pavillon Roger-Gaudry H307-7
      (514) 343-6111 ext. 2721
http://megasun.bch.umontreal.ca/People/ahauth

Bioinformatic Tools

Note: Current versions were coded to optimize for development trial-and-error. If you are interested in creating a better (more efficient) implementation for these algorithms, please contact the author!

ComplexTR (Web access, download command line software - beta version 1.2.0)

    Current Release: 1.2.0
    Release Date: July 25, 2005

    Please Reference
    Hauth, A.M. and Joseph, D.A.
    Beyond Tandem Repeats: Complex Pattern Structures and Distant Regions of Similarity.
    Bioinformatics. 2002 Jul;18 Suppl 1:S31-7.

    Basic Description:
    To identify and characterize tandem repeats having simple and complex pattern structures including but not limited to
    • Simple sequence repeats (SSRs)
    • Variable length tandem repeats (VLTR)
    • Multi-periodic tandem repeats (MPTR)

    Input: DNA sequence
    Output: HTML page with detailed characterization of each tandem repeat region

    Source Code: (C++, perl)
    • Tandem repeat identification code (C++)
    • Web Interface via CGI scripts (perl)

TRIplot (download alpha version 1.0.1)

    Current Release: 1.0.1
    Release Date: July 29, 2004

    Please Reference
    Amy M. Hauth, Robert-Cedergren Center, Université de Montréal, Montréal, QC, Canada

    Basic Description: To facilitate identification of sequence similar regions within sequences through identification of imperfect direct and inverse repeats

    Input:
    • DNA sequence
    • Expert-defined files with sequence positions of interest (optional)
    Output: Display of direct and inverse repeats that occur within sequences
    • TriPlot (triangular dot plot) – a PNG triangle (half of a square) with each edge of the triplot representing positions within the sequence.
    • GridPlot– a text based grid that lines up sequence-similar direct and inverse repeats within the sequence. The horizontal axis represents positions along the sequence. The top line of the vertical axis contains the nucleotides that occur at each sequence position. The lines below the nucleotide-level sequence display sequence-similar regions indicating matches (uppercase) and mismatches (lowercase), direction of similarity (direct or inverse) and positions of similarity

    Source Code: (C, C++, perl, csh)
    • Direct and inverse repeat search engine (C)
      Huang, Y. and Zhang, L. Bioinformatics 2004 Mar 1;20(4):460-6.
    • Search engine and data structure wrappers (C++)
    • Plotting scripts (perl)
    • Execution scripts (csh shell scripts)