Sequence Analysis - Bioinformatics - Accelerating Pine Genomics - APG - NSF DBI-0421717 - Daniel G. Peterson

Shotgun Sequence Analysis Pipeline (SSAP) - We have developed a "Shotgun Sequence Analysis Pipeline" (SSAP) to permit automated characterization of a genome based on random shotgun reads. The SSAP also represents a standardized means by which the efficiency of reduced-representation sequencing techniques can be accessed. The SSAP is composed of many novel Perl and DTS scripts that have been integrated with existing bioinformatics software (e.g., BLAST, Phred, and CAP3) and local sequence databases to create a complex and powerful genome characterization tool. A manuscript describing the resulting 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 APG Software webpage. A model of the SSAP (under continual revision) with access to spermatophyte-specific sequence databases can be explored by clicking here.

Other sequencing pipelines, including a "BAC Sequence Assembly Pipeline" (BSAP) and a "Repeat Sequence Analysis Pipeline" (RSAP), are under construction.

Other Bioinformatics Topics: LIMS | Algorithm & Software Development | Intranet Development


	Shotgun Sequence Analysis Pipeline (SSAP) - We have developed a "Shotgun Sequence Analysis Pipeline" (SSAP) to permit automated characterization of a genome based on random shotgun reads. The SSAP also represents a standardized means by which the efficiency of reduced-representation sequencing techniques can be accessed. The SSAP is composed of many novel Perl and DTS scripts that have been integrated with existing bioinformatics software (e.g., BLAST, Phred, and CAP3) and local sequence databases to create a complex and powerful genome characterization tool. A manuscript describing the resulting 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 APG Software webpage. A model of the SSAP (under continual revision) with access to spermatophyte-specific sequence databases can be explored by clicking here. Other sequencing pipelines, including a "BAC Sequence Assembly Pipeline" (BSAP) and a "Repeat Sequence Analysis Pipeline" (RSAP), are under construction. Other Bioinformatics Topics: LIMS \| Algorithm & Software Development \| 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.