Absolute Genomic Position

Abstract Motivation Computing the uniqueness of k-mers for each position of a genome while allowing for up to e mismatches is computationally challenging. However, it is crucial for many biological applications such as the design of guide RNA for CRISPR experiments. More formally, the uniqueness or (k, e)-mappability can be described for every position as the reciprocal value of how often this k-mer occurs approximately in the genome, i.e. with up to e mismatches. Results We present a fast method GenMap to compute the (k, e)-mappability. We extend the mappability algorithm, such that it can also be computed across multiple genomes where a k-mer occurrence is only counted once per genome. This allows for the computation of marker sequences or finding candidates for probe design by identifying approximate k-mers that are unique to a genome or that are present in all genomes. GenMap supports different formats such as binary output, wig and bed files as well as csv files to export the location of all approximate k-mers for each genomic position. Availability and implementation GenMap can be installed via bioconda. Binaries and C++ source code are available on https://github.com/cpockrandt/genmap.

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GPAT: Retrieval of genomic annotation from large genomic position datasets

BMC Bioinformatics ◽

10.1186/1471-2105-9-533 ◽

2008 ◽

Vol 9 (1) ◽

Cited By ~ 20

Author(s):

Arnaud Krebs ◽

Mattia Frontini ◽

Làszlò Tora

Keyword(s):

Genomic Position ◽

Genomic Annotation

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The effect of genomic position on reversion of a lac frameshift mutation (lacIZ33) during non-lethal selection (adaptive mutation)

Molecular Microbiology ◽

10.1046/j.1365-2958.2002.02934.x ◽

2002 ◽

Vol 44 (4) ◽

pp. 1017-1032 ◽

Cited By ~ 24

Author(s):

E. Susan Slechta ◽

Jennifer Harold ◽

Dan I. Andersson ◽

John R. Roth

Keyword(s):

Frameshift Mutation ◽

Adaptive Mutation ◽

Genomic Position

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HP1a, Su(var)3-9, SETDB1 and POF stimulate or repress gene expression depending on genomic position, gene length and expression pattern in Drosophila melanogaster

Nucleic Acids Research ◽

10.1093/nar/gkt158 ◽

2013 ◽

Vol 41 (8) ◽

pp. 4481-4494 ◽

Cited By ~ 28

Author(s):

Lina E. Lundberg ◽

Per Stenberg ◽

Jan Larsson

Keyword(s):

Gene Expression ◽

Drosophila Melanogaster ◽

Expression Pattern ◽

Gene Length ◽

Genomic Position

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Coronaviruses as Vectors: Position Dependence of Foreign Gene Expression

Journal of Virology ◽

10.1128/jvi.77.21.11312-11323.2003 ◽

2003 ◽

Vol 77 (21) ◽

pp. 11312-11323 ◽

Cited By ~ 51

Author(s):

Cornelis A. M. de Haan ◽

Linda van Genne ◽

Jeroen N. Stoop ◽

Haukeline Volders ◽

Peter J. M. Rottier

Keyword(s):

Gene Expression ◽

Expression Vectors ◽

Luciferase Expression ◽

Foreign Gene ◽

Regulatory Sequences ◽

Expression Levels ◽

Genomic Position ◽

Position Dependence ◽

Foreign Genes

ABSTRACT Coronaviruses are the enveloped, positive-stranded RNA viruses with the largest RNA genomes known. Several features make these viruses attractive as vaccine and therapeutic vectors: (i) deletion of their nonessential genes is strongly attenuating; (ii) the genetic space thus created allows insertion of foreign information; and (iii) their tropism can be modified by manipulation of the viral spike. We studied here their ability to serve as expression vectors by inserting two different foreign genes and evaluating systematically the genomic position dependence of their expression, using a murine coronavirus as a model. Renilla and firefly luciferase expression cassettes, each provided with viral transcription regulatory sequences (TRSs), were inserted at several genomic positions, both independently in different viruses and combined within one viral genome. Recombinant viruses were generated by using a convenient method based on targeted recombination and host cell switching. In all cases high expression levels of the foreign genes were observed without severe effects on viral replication in vitro. The expression of the inserted gene appeared to be dependent on its genomic position, as well as on the identity of the gene. Expression levels increased when the luciferase gene was inserted closer to the 3′ end of the genome. The foreign gene insertions generally reduced the expression of upstream viral genes. The results are consistent with coronavirus transcription models in which the transcription from upstream TRSs is attenuated by downstream TRSs. Altogether, our observations clearly demonstrate the potential of coronaviruses as (multivalent) expression vectors.

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