TY - JOUR

T1 - Frameshift detection in prokaryotic genomic sequences

AU - Kislyuk, Andrey

AU - Lomsadze, Alexandre

AU - Lapidus, Alla L.

AU - Borodovsky, Mark

PY - 2009/7

Y1 - 2009/7

N2 - We have developed a new method for frameshift detection, a combination of ab initio and alignment-based algorithms, that can serve as a useful tool for sequencing quality control in the next generation sequencing. We evaluated the method's accuracy on test sets of annotated genomic sequences with artificial frameshifts in protein coding regions. These tests have shown that the new method performs comparably to the earlier developed FrameD. On the sets of sequences produced by 454 pyrosequencing with sequence errors recovered by Sanger re-sequencing the accuracy of the method was shown to hold at the same level.

AB - We have developed a new method for frameshift detection, a combination of ab initio and alignment-based algorithms, that can serve as a useful tool for sequencing quality control in the next generation sequencing. We evaluated the method's accuracy on test sets of annotated genomic sequences with artificial frameshifts in protein coding regions. These tests have shown that the new method performs comparably to the earlier developed FrameD. On the sets of sequences produced by 454 pyrosequencing with sequence errors recovered by Sanger re-sequencing the accuracy of the method was shown to hold at the same level.

KW - Frameshift

KW - Genomics

KW - Hidden Markov model

KW - HMM

KW - Machine learning

KW - Markov chains

KW - Pyrosequencing

KW - Sensitivity

KW - Sn

KW - Sp

KW - Specificity

UR - http://www.scopus.com/inward/record.url?scp=68949217682&partnerID=8YFLogxK

U2 - 10.1504/IJBRA.2009.027519

DO - 10.1504/IJBRA.2009.027519

M3 - Article

C2 - 19640832

AN - SCOPUS:68949217682

VL - 5

SP - 458

EP - 477

JO - International Journal of Bioinformatics Research and Applications

JF - International Journal of Bioinformatics Research and Applications

SN - 1744-5485

IS - 4

ER -