scholarly journals Absolute Genomic Position

2020 ◽  
Author(s):  
Keyword(s):  
Genomic Position

scholarly journals GenMap: ultra-fast computation of genome mappability

2020 ◽  
Vol 36 (12) ◽  
pp. 3687-3692 ◽  
Author(s):  
Christopher Pockrandt ◽  
Mai Alzamel ◽  
Costas S Iliopoulos ◽  
Knut Reinert
Keyword(s):  
Source Code ◽  
Probe Design ◽  
Fast Method ◽  
Biological Applications ◽  
Fast Computation ◽  
Genomic Position ◽  
Guide Rna ◽  
Binary Output ◽  
A Genome ◽  
Reciprocal Value

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.

scholarly journals GPAT: Retrieval of genomic annotation from large genomic position datasets

2008 ◽  
Vol 9 (1) ◽  
Author(s):  
Arnaud Krebs ◽  
Mattia Frontini ◽  
Làszlò Tora
Keyword(s):  
Genomic Position ◽  
Genomic Annotation

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

2002 ◽  
Vol 44 (4) ◽  
pp. 1017-1032 ◽  
Author(s):  
E. Susan Slechta ◽  
Jennifer Harold ◽  
Dan I. Andersson ◽  
John R. Roth
Keyword(s):  
Frameshift Mutation ◽  
Adaptive Mutation ◽  
Genomic Position

scholarly journals Coronaviruses as Vectors: Position Dependence of Foreign Gene Expression

2003 ◽  
Vol 77 (21) ◽  
pp. 11312-11323 ◽  
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.

scholarly journals Using a priori knowledge to align sequencing reads to their exact genomic position

2012 ◽  
Vol 40 (16) ◽  
pp. e125-e125 ◽  
Author(s):  
René Böttcher ◽  
Ronny Amberg ◽  
F. P. Ruzius ◽  
V. Guryev ◽  
Wim F. J. Verhaegh ◽  
...  
Keyword(s):  
A Priori ◽  
A Priori Knowledge ◽  
Genomic Position ◽  
Priori Knowledge

Genomic position influences spontaneous mutagenesis of an integrated retroviral vector containing the hprt cDNA as target for mutagenesis

1993 ◽  
Vol 2 (2) ◽  
pp. 173-182 ◽  
Author(s):  
Elgin G.R. Lichtenauer-Kaligis ◽  
letje van der Velde-van Dijke ◽  
Hans den Dulk ◽  
Pieter van de Putte ◽  
Micheline Giphart-Gassler ◽  
...  
Keyword(s):  
Retroviral Vector ◽  
Spontaneous Mutagenesis ◽  
Genomic Position

scholarly journals Genomic position affects the expression of tobacco mosaic virus movement and coat protein genes.

1993 ◽  
Vol 90 (5) ◽  
pp. 2055-2059 ◽  
Author(s):  
J. N. Culver ◽  
K. Lehto ◽  
S. M. Close ◽  
M. E. Hilf ◽  
W. O. Dawson
Keyword(s):  
Coat Protein ◽  
Tobacco Mosaic Virus ◽  
Mosaic Virus ◽  
Virus Movement ◽  
Genomic Position

scholarly journals Genomic Position Mapping Discrepancies of Commercial SNP Chips

PLoS ONE ◽  
2012 ◽  
Vol 7 (2) ◽  
pp. e31025 ◽  
Author(s):  
João Fadista ◽  
Christian Bendixen
Keyword(s):  
Genomic Position

Genomic position analyses and the transcription machinery 1 1Edited by M. Yahiv

1998 ◽  
Vol 275 (2) ◽  
pp. 165-170 ◽  
Author(s):  
Ernesto Pérez-Rueda ◽  
Jay D. Gralla ◽  
Julio Collado-Vides
Keyword(s):  
Genomic Position ◽  
Transcription Machinery
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