Title:	Identification of 20-mer absent from hg19 using BLAT
DNr:	SNIC 2016/1-237
Project Type:	SNIC Medium Compute
Principal Investigator:	Magda Bienko <magda.bienko@ki.se>
Affiliation:	Karolinska Institutet
Duration:	2016-05-01 – 2016-09-01
Classification:	10604
Keywords:

Abstract

In 2009, Xu et al. (Xu, PNAS 2009) published a list of 240000 25mer DNA barcode probes orthogonal to mammalian genomes. These barcodes can be used in a variety of applications, one of which is the selection of subsets of oligonucleotides from array-synthesized oligonucleotide pools. To perform such operation, each oligonucleotide is originally designed with two barcodes at its extremities, and sub-pools of oligonucleotides are selectively amplified via PCR by using a set of forward/reverse primers complementary to the aforementioned barcodes. In order to keep the length of the oligonucleotides in the pool as short as possible, rendering their synthesis less expensive and reducing the number of errors expected during this process, we are designing 20-mer barcodes starting from the 240000 25-mers list published by Xu et al. We have already generated the unique 1200000 20-mers from Xu’s list, and we are interested in the identification of all the 20-mers with a maximum homology of 70% (14 nt) to hg19. We have already identified a set of parameters that renders BLAT suitable for this task, and we have run a small subset (6k out of 1.2M) of the unique 20-mers against hg19 and identified their best matches.