ARS | Publication request: HYBSWEEPER: A RESOURCE FOR DETECTING HIGH-DENSITY PLATE COORDINATES

Submitted to: Biotechniques
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 14, 2005
Publication Date: September 1, 2005
Citation: Lazo, G.R., Lui, N., Gu, Y.Q., Kong, X., Coleman Derr, D., Anderson, O.D. 2005. Hybsweeper: a resource for detecting high-density plate coordinates. Biotechniques. 39:320-324.

Interpretive Summary: A software tool was developed to speed processing of information gained from DNA hybridization patterns stamped to high-density grids. The gridding patterns matched to clones which were housed in microtiter dishes. High-throughput methodologies have made it increasingly difficult to work with large archives of stored resources. The method developed to ease this effort was a software package called Hybsweeper, and was applied to laboratory work associated with simple probing methods, overgo probe hybridizations, and isolation of unique clones from saturation hybridization conditions.

Technical Abstract: A software tool was developed to handle images of high-density gridding patterns which were matched to clones housed in microtiter dishes. As high-throughput methodologies contribute to large archives of stored resources, methods need to be available for convenient processing of hybridization information for the retrieval of the clones needed for research endeavors. The development of the software was done in conjunction with laboratory research focused around a 516,256 clone BAC genomic library of the 13,500 Mb genome of durum wheat (Triticum turgidum subsp. durum). The java program utilized DNA-DNA hybridization experimental data replicated to nylon filters using a Genetic Q-bot arraying system.