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United States Department of Agriculture

Agricultural Research Service

Title: Database Management of High Throughput Est Sequencing and Snp Discovery

Authors
item KEELE, JOHN
item Wray Jr, James
item SMITH, TIMOTHY
item Fahrenkrug, Scott
item CASAS, EDUARDO
item FREKING, BRADLEY
item Stone, Roger

Submitted to: Journal of Animal Science Supplement
Publication Type: Abstract Only
Publication Acceptance Date: May 30, 2000
Publication Date: N/A

Technical Abstract: The human genome sequence is gradually being deposited in GenBank at the National Center for Biotechnology Information (NCBI). Comparative maps between human and livestock genomes are expected to accelerate the development of technologies to improve production efficiency, product quality and food safety. Low-cost, high-throughput genotyping for a large number of SNP distributed across the genome is expected to increase the number of quantitative trait loci (QTL) that are detected and improve the effectiveness of marker-assisted selection. Progress would be accelerated by database and bioinformatics technologies capable of assimilating large volumes of data in heterogenous formats distributed across a computer network with minimal human intervention. The objectives of the work reported here were to sequence 80,000 EST for cattle and 40,000 for pigs, automate comparisons between livestock and human sequences and automate primer design targeting amplification of intron sequences. The EST are being generated from 6 normalized cDNA libraries (4 from bovine and 2 from swine). Sequencing was done with a 3700 ABI sequencer. Automation of BLAST and capturing results into a local database required minimal human intervention (< 1 intervention / 10,000 query sequences). The comparison of livestock EST with human genomic sequence using BLAST was used to predict the length and position of introns. Primers were designed flanking predicted introns using Primer3. Automation of the primer design process required minimal human intervention (< 1 intervention / 10,000 sequences). In conclusion, automation of analytical processes required for EST sequencing projects is feasible and facilitates increased throughput and more rapid progress.

Last Modified: 8/19/2014
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