how does Agilent/xGen design hybridization probes?

Question

[bitpir]

I'm curious about how Agilent/IDT design exome hybridization probes, how do they ensure that (i)the probes won't self-anneal, (ii) mostly capturing exonic regions, (iii) GC content and (iv) annealing temp of each probe to fragmented DNA are similar? Is there a free software (like PCRTiler) available for use?

Answer 1

[jean.elbers]

I wrote a small description of how MYcroarray (now Arbor Biosciences) designed probes back in 2014-2015 in the following paper https://www.researchgate.net/publication/283881559_GO2TR_a_gene_ontology-based_workflow_to_generate_target_regions_for_target_enrichment_experiments, (see the section called GO2TR’s utility for non-model organisms: in silico analysis). Their exact practices may have changed, but my description at least includes the most salient features of bait/probe design.

[bitpir]

Excellent, this is what I'm looking for! Thank you so much :)