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Hybdecon was developed to reduce the complexity of the multi-dimensional pooling analysis. It is a stand-alone Java and Perl application that provides an easy-to-use interface for manually calling of hits on a pooled array and deconvolution of those hits. The program generates an ACE file for loading markers into FPC. The software also provides image loading and processing functions to aid in manual calling and users can stop, save and resume their work at any time.
The graphical user-interface is derived from HybSweeper (Lazo et al. Biotechniques 39:320, 2005) a web-based screening tool. The Perl deconvolution script was developed entirely at CUGI.
Hybridization screening methods can be used to map genetic markers to BACs and in turn anchor those markers onto a physical map, creating an integrated physical and genetic map. The integrated map can be used to assist with the design of sequencing strategies and assembly of complete genomes. Multi-dimensional hybridization pooling strategies have been employed to reduce the time and cost of hybridizations, but require a deconvolution step to tease out one-to-one mappings.
How to Install and Launch Hybdecon
java -jar Hybdecon-0.1.jar
CUGI offers an online tool for assistance with setup of the pooling experiment. You can upload you probes and indicate the number of dimensions and pools you desire. The tool will generate all files necessary for the deconvolution as well as provide files for the lab that indicate which probes should be placed in each pool. the link for this tool can be found here: Pooling Experiment Setup.
Hybdecon should run smoothly under the following specifications:
HybDecon was used in a Chinese Chestnut (Castanea mollissima) hybridization experiment with 3 dimensions and 125 overgos. This work was funded by the NSF grant Genomic Tool Development for the Fagaceae (NSF-PGRP 0605135). Probes were individually labeled and compiled into 15 pools. Four filters were required for a single copy of two Chinese Chestnut BAC libraries. With a set of filters hybridized for each pool, a total of 120 filter images were created and individually called with HybDecon. Hybridizations were performed at 60 degree overnight, and BAC filters were washed with 0.1% SDS and 1X SSC at 60 degrees. Images of the hybridizations were recorded by phosphor screens and read by a Typhoon 9400 imager (GE Healthcare, Piscataway, NJ, USA). A total of 124 probes were successfully associated with at least one BAC clone by the deconvolution function of HybDecon.
Main output files from deconvolution:
Deconvolution output files with contigs that were unable to be deconvoluted: