CotQuest - Version
Reference: Bunge JA, Chouvarine P, Peterson DG (2008) CotQuest: Improved algorithm and software for nonlinear regression analysis of DNA reassociation kinetics data, submitted.
Description: CotQuest is specifically tailored to conduct nonlinear regression analysis of DNA reassociation kinetics (i.e., Cot) data when used with the statistics package SAS® (www.sas.com). CotQuest is unique in that it does not require users to input guesses as to the final values of parameters. The CotQuest program surpasses all existing Cot analysis programs with regard to automation, statistical robustness, user-friendliness, and graphical output. CotQuest is available in two variations, CotQuestG and CotQuestU.
User Guide: CotQuest User's Guide (pdf)
CotQuestG, v1.0 - For use with Windows XP or Windows Vista. CotQuestG is packaged with a graphical user interface (GUI) that helps lead users through the Cot analysis process.
CotQuestU, v1.0 - For use on all operating systems that are compatible with SAS® (i.e., Windows, Unix, Linux, and Macintosh). CotQuestU does not have a GUI.
Pseudo-code (pdf) - For those interested in adapting the CotQuest algorithms for use with 'R' and/or other statistics packages
Sequence Read Classification
Pipeline (SRCP) - Version 1.0
Reference: Chouvarine P, Saha S, Peterson DG (2008) An automated, high-throughput sequence read classification pipeline for preliminary genome characterization. Analytical Biochemistry 373: 78-87 - see Publications
Description: The SRCP is a high-throughput, automated data analysis pipeline that is used to classify genomic shotgun reads into functional/descriptive sequence categories. It represents a powerful means of rapidly describing the sequence content of a genome and a standardized method for estimating gene/repeat enrichment or reduction afforded by Cot filtration, CBCS, and/or other reduced-representation sequencing (RRS) techniques (see Peterson 2005 for review of RRS methods).
Perl Scripts: Ace2XmlContigsOnly.pl | blast2flatxml.pl | Blast2HighScoreList.pl | fastaFilter.pl | fastaMergerAndFilter.pl | GroupAce2Xml.pl | PhredFilter.pl | RepeatRegionExtractor.pl | SelfBlast2RepQSList.pl | SelfBlast2RepQSList_MidCoverage.pl
DTS Scripts: BulkUploadExample_DTS.txt | Example.xsd | Top3to1row_DTS.txt
SQL Queries: PossibleRepeatsQueries.txt | ProbableRepeatQueries.txt
Local Sequence Databases (LDBs): Mitochondria | Chloroplast | Transposon | EMC | Gene Index | Centromere | rDNA | Annotated Repeat