Drndić and her colleagues tested their silicon nitride nanopore
on homopolymers, or single strands of DNA with sequences that consist of only one base repeated several times.
They did not attempt to measure guanine
as homopolymers made with that base bind back on themselves, making it more difficult to pass them through the nanopores.
An illustration of a single - stranded
DNA homopolymer translocating through a silicon nitride nanopore.
Multiple incorporations cause linear increases in the pH change,
so homopolymers should be less of a problem than 454.
pencil: bees wax, hydrogenated palm kernel glycerides (and) hydrogenated palm glycerides, rhus succedanea fruit wax, butyrospermum parkii (shea butter), talc, carnauba wax, castor oil, isopropyl myristate, butylparaben, bht gel: pure water, ammonium methacrylate copolymer, dimethicone, kaolin, peg - 30 dipolyhydroxystearate,
polyethylene homopolymer, propolis, decamethylcyclopentasiloxane (ss4230), panthenol, 1,2 - hexanediol (symdiol ® 68t), hyaluronic acid
These might arise from a number of causes —
homopolymers, paralogs, repeats, sequencing error, alignment error, etc..
On the 454, it's
homopolymers — stretches of A's, C's, G's, or T's four or more bases long.
There's even a SAM / BAM converter for 454 data, which sounds like a dicey prospect given
the homopolymer undercalling / overcalling problem.
Many can be filtered, but often
homopolymer - associated errors cause mis - alignment of reads, yielding indels that might not look like homopolymer artifacts.