XSTREAM

Description

  • XSTREAM is a powerful genome data-mining tool designed to efficiently identify Tandem Repeat (TR) patterns in biological sequence data. The program uses a seed-extension strategy coupled with several post-processing algorithms to analyze FASTA-formatted protein or nucleotide sequences. XSTREAM uses a number of user-defined parameters to identify non-redundant TR sequences with diverse periods and domain sizes, and varied levels of degeneracy. Additionally, the program effectively merges discontinuous TRs into larger TR domains, clusters similar TR sequences, models TR domain architectures, and detects hierarchical TR patterns.

    If you use XSTREAM, please cite Newman and Cooper, BMC Bioinformatics 2007.

    • Software

    XSTREAM is coded in Java.

    Input

    FASTA formatted sequence(s). To process multiple sequences, make a list of all FASTA input sequences and save them as a text file.

    Download

    Click here. Simply uncompress the contents of xstream.zip into the same directory and follow the instructions in XSTREAMdoc.pdf to run XSTREAM.

    Web server

    Down until further notice (last update: 08-17-2023).