Base-calling algorithm with vocabulary (BCV) method for analyzing population sequencing chromatograms.

ABSTRACT: Sanger sequencing is a common method of reading DNA sequences. It is less expensive than high-throughput methods, and it is appropriate for numerous applications including molecular diagnostics. However, sequencing mixtures of similar DNA of pathogens with this method is challenging. This is important because most clinical samples contain such mixtures, rather than pure single strains. The traditional solution is to sequence selected clones of PCR products, a complicated, time-consuming, and expensive procedure. Here, we propose the base-calling with vocabulary (BCV) method that computationally deciphers Sanger chromatograms obtained from mixed DNA samples. The inputs to the BCV algorithm are a chromatogram and a dictionary of sequences that are similar to those we expect to obtain. We app

SUBMITTER: Fantin YS 

PROVIDER: S-EPMC3557274 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature