Shotgun Sequence Analysis Pipeline (SSAP) - Many novel Perl and DTS scripts have been integrated with existing bioinformatics standards (e.g., BLAST, Phred, and CAP3) to create a complex and powerful genome characterization tool.  A manuscript describing the resulting "Shotgun Sequence Analysis Pipeline" (SSAP) is nearing completion (anticipated submission date of July 1, 2006) while a manuscript detailing its use in characterizing the pine genome is in the early stages of preparation.  Once the first SSAP manuscript is accepted for publication, the SSAP scripts and/or source codes will be made available through the Software webpage.  A model of the SSAP (under continual revision) with access to spermatophyte-specific sequence databases can be explored by clicking here.

Cot Analysis Program - This program is essentially an updated version of the one developed by Pearson et al. (1977).  Of note, a mathematical error in the original program of Pearson et al. has been detected and corrected.  Our C++ Cot analysis script is now in working order, but needs to be made more user-friendly before release on the Software webpage.

Other Bioinformatics Topics: LIMS | Sequence Analysis | Intranet Development

*This material is based upon work supported by the National Science Foundation under Grant No. DBI-0421717.  Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.  MGEL © 2006. Web design by Daniel G. Peterson.  Last updated 08-Jun-2006.