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Searching of Conserved Motfs within a Partal secA Gene Sequence of Phytoplasma Associated with Root (Wilt) Disease of Coconut (Cocos nucifera) in India: Usinga Frequency Based Approach

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Title Searching of Conserved Motfs within a Partal secA Gene Sequence of Phytoplasma Associated with Root (Wilt) Disease of Coconut (Cocos nucifera) in India: Usinga Frequency Based Approach
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Creator Sandip Shil, Kishore K. Das and Anamika Dutta
 
Subject Coconut disease, conserved region, information content, PWM, motif
 
Description Not Available
Coconut palm (Cocos nucifera L.) root (wilt) disease (CRWD) became a serious concern for coconut cultivation in coastal region of India. Due to which, India looses a considerable economic loss of about 968 million nuts, annually. The disease is non lethal. It has already been reported that species of the phytoplasmas, belonging to ribosomal group 16SrXI, are primarily associated with CRWD. In the current study, our objective is to identify motif that describes the conserved region within protein sequence of CRWD. Due to variations of amino acid residues at given positions within a positional weight matrix (PWM), the pattern of protein sequence motif can be identified using a multinomial probabilistic model. The basic assumption underlying this model is that the amino acid residues within a sequence are independent and identically distributed. To determine the overall probability of that PWM, the formula for computing information content or relative entropy may also be used. Here, such measure has been proposed to identify motifs within PWM, in this paper. Finally, various conserved motifs within the partial secA gene sequence of phytoplasma associated with CRWD, using that measure, have been successfully identified. On the basis of obtained results, we reached to conclusions that conserved regions or motifs (of different length) are expected to be found at (163-171) and (120-138) positions of within that partial secA gene sequence.
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Date 2018-11-26T08:49:55Z
2018-11-26T08:49:55Z
2015-11-01
 
Type Journal
 
Identifier Not Available
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http://krishi.icar.gov.in/jspui/handle/123456789/13422
 
Language English
 
Relation Not Available;
 
Publisher International Journal of Bio-resource and Stress Management