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CotQuest | Sequence Read Classification Pipeline (SRCP)
CotQuest - Version
1.0
Reference: Bunge JA, Chouvarine P, Peterson DG (2009) CotQuest:
Improved algorithm and software for nonlinear regression analysis of DNA
reassociation kinetics data. Analytical Biochemistry, in press.
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)
Download Program:
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.
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
Algorithms:
DecisionTree.txt
Local Sequence Databases (LDBs):
Mitochondria |
Chloroplast |
Transposon | EMC |
Gene Index |
Centromere |
rDNA |
Annotated
Repeat