Biomaterial Database

Frameshift detection in prokaryotic genomic sequences. 2009

Andrey Kislyuk, and Alexandre Lomsadze, and Alla L Lapidus, and Mark Borodovsky

School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA. kislyuk@gatech.edu

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.

UI	MeSH Term	Description	Entries
D000465	Algorithms	A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.	Algorithm
D016366	Open Reading Frames	A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).	ORFs,Protein Coding Region,Small Open Reading Frame,Small Open Reading Frames,sORF,Unassigned Reading Frame,Unassigned Reading Frames,Unidentified Reading Frame,Coding Region, Protein,Frame, Unidentified Reading,ORF,Open Reading Frame,Protein Coding Regions,Reading Frame, Open,Reading Frame, Unassigned,Reading Frame, Unidentified,Region, Protein Coding,Unidentified Reading Frames
D016368	Frameshift Mutation	A type of mutation in which a number of NUCLEOTIDES deleted from or inserted into a protein coding sequence is not divisible by three, thereby causing an alteration in the READING FRAMES of the entire coding sequence downstream of the mutation. These mutations may be induced by certain types of MUTAGENS or may occur spontaneously.	Mutation, Frameshift,Frame Shift Mutation,Out-of-Frame Deletion,Out-of-Frame Insertion,Out-of-Frame Mutation,Deletion, Out-of-Frame,Deletions, Out-of-Frame,Frame Shift Mutations,Frameshift Mutations,Insertion, Out-of-Frame,Insertions, Out-of-Frame,Mutation, Frame Shift,Mutation, Out-of-Frame,Mutations, Frame Shift,Mutations, Frameshift,Mutations, Out-of-Frame,Out of Frame Deletion,Out of Frame Insertion,Out of Frame Mutation,Out-of-Frame Deletions,Out-of-Frame Insertions,Out-of-Frame Mutations
D016415	Sequence Alignment	The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.	Sequence Homology Determination,Determination, Sequence Homology,Alignment, Sequence,Alignments, Sequence,Determinations, Sequence Homology,Sequence Alignments,Sequence Homology Determinations
D016680	Genome, Bacterial	The genetic complement of a BACTERIA as represented in its DNA.	Bacterial Genome,Bacterial Genomes,Genomes, Bacterial
D023281	Genomics	The systematic study of the complete DNA sequences (GENOME) of organisms. Included is construction of complete genetic, physical, and transcript maps, and the analysis of this structural genomic information on a global scale such as in GENOME WIDE ASSOCIATION STUDIES.	Functional Genomics,Structural Genomics,Comparative Genomics,Genomics, Comparative,Genomics, Functional,Genomics, Structural