scholarly journals Positive Selection Analysis of Overlapping Reading Frames Is Invalid

2015 ◽  
Vol 31 (10) ◽  
pp. 947-947 ◽  
Author(s):  
Christopher Monit ◽  
Richard A. Goldstein ◽  
Greg Towers ◽  
Stéphane Hué
Keyword(s):  
Positive Selection ◽  
Selection Analysis ◽  
Overlapping Reading Frames ◽  
Reading Frames

scholarly journals Overlapping reading frames in Oenothera mitochondria

FEBS Letters ◽  
1985 ◽  
Vol 193 (2) ◽  
pp. 164-168 ◽  
Author(s):  
Rudolf Hiesel ◽  
Axel Brennicke
Keyword(s):  
Overlapping Reading Frames ◽  
Reading Frames

scholarly journals Designing a Bioengine for Detection and Analysis of Base String on an Affected Sequence in High-Concentration Regions

2013 ◽  
Vol 2013 ◽  
pp. 1-7
Author(s):  
Debnath Bhattacharyya ◽  
Bijoy Kumar Mandal ◽  
Tai-hoon Kim
Keyword(s):  
Query Sequence ◽  
Sequence Length ◽  
Biological Sequences ◽  
Normal Plant ◽  
High Concentration ◽  
Front End ◽  
Overlapping Reading Frames ◽  
Optimal Alignments ◽  
High Degree ◽  
Reading Frames

We design an Algorithm for bioengine. As a program are enable optimal alignments searching between two sequences, the host sequence (normal plant) as well as query sequence (virus). Searching for homologues has become a routine operation of biological sequences in 4 × 4 combination with different subsequence (word size). This program takes the advantage of the high degree of homology between such sequences to construct an alignment of the matching regions. There is a main aim which is to detect the overlapping reading frames. This program also enables to find out the highly infected colones selection highest matching region with minimum gap or mismatch zones and unique virus colones matches. This is a small, portable, interactive, front-end program intended to be used to find out the regions of matching between host sequence and query subsequences. All the operations are carried out in fraction of seconds, depending on the required task and on the sequence length.

scholarly journals Cloning, Expression, and Site-Directed Mutagenesis of the Propene Monooxygenase Genes from Mycobacterium sp. Strain M156

2005 ◽  
Vol 71 (4) ◽  
pp. 1909-1914 ◽  
Author(s):  
Chan K. Chan Kwo Chion ◽  
Sarah E. Askew ◽  
David J. Leak
Keyword(s):  
Mutational Analysis ◽  
Substrate Binding ◽  
Site Directed Mutagenesis ◽  
Side Chain ◽  
Directed Mutagenesis ◽  
Active Site Residues ◽  
Styrene Oxidation ◽  
Overlapping Reading Frames ◽  
Reading Frames

ABSTRACT Propene monooxygenase has been cloned from Mycobacterium sp. strain M156, based on hybridization with the amoABCD genes of Rhodococcus corallinus B276. Sequencing indicated that the mycobacterial enzyme is a member of the binuclear nonheme iron monooxygenase family and, in gene order and sequence, is most similar to that from R. corallinus B-276. Attempts were made to express the pmoABCD operon in Escherichia coli and Mycobacterium smegmatis mc2155. In the former, there appeared to be a problem resolving overlapping reading frames between pmoA and -B and between pmoC and -D, while in the latter, problems were encountered with plasmid instability when the pmoABCD genes were placed under the control of the hsp60 heat shock promoter in the pNBV1 vector. Fortuitously, constructs with the opposite orientation were constitutively expressed at a level sufficient to allow preliminary mutational analysis. Two PMO active-site residues (A94 and V188) were targeted by site-directed mutagenesis to alter their stereoselectivity. The results suggest that changing the volume occupied by the side chain at V188 leads to a systematic alteration in the stereoselectivity of styrene oxidation, presumably by producing different orientations for substrate binding during catalysis. Changing the volume occupied by the side chain at A94 produced a nonsystematic change in stereoselectivity, which may be attributable to the role of this residue in expansion of the binding site during substrate binding. Neither set of mutations changed the enzyme's specificity for epoxidation.

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