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Kumar, Akash
- Evolutionary Analysis and Motif Discovery in Pinopsin from Vertebrates
Abstract Views :672 |
PDF Views:370
Authors
Affiliations
1 Department of Bioinformatics, Uttaranchal College of Science & Technology, Dehradun, IN
2 Department of Biotechnology, Uttaranchal College of Science & Technology, Dehradun, IN
3 Forest Pathology Division, Forest Research Institute, Dehradun, IN
1 Department of Bioinformatics, Uttaranchal College of Science & Technology, Dehradun, IN
2 Department of Biotechnology, Uttaranchal College of Science & Technology, Dehradun, IN
3 Forest Pathology Division, Forest Research Institute, Dehradun, IN
Source
Indian Journal of Bioinformatics and Biotechnology, Vol 2, No 3 (2013), Pagination: 65-68Abstract
In the present investigation, total nine protein sequences of Pinopsin from different organisms of vertebrates were obtained from GenPept database and only 347 characters of each sequence were considered for motif discovery, motif family analysis and phylogenetic analysis. Three different motifs were discovered by MEME program where minimum motif width was 6 and maximum motif width was 50. All three discovered motifs were aligned using MAST tool which revealed the similarity between all of three submitted motif's sequence. The motif matches shown have a position p-value less than 0.0001. Each of the following 9 sequences has an E-value less than 10. Two major sequence clusters were constructed by phylogenetic analysis.References
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- Analytical Study of Plasmodium Yoelii Yoelii
Abstract Views :627 |
PDF Views:377
Authors
Affiliations
1 Department of Bioinformatics , Uttaranchal College of Science & Technology, Dehradun, IN
1 Department of Bioinformatics , Uttaranchal College of Science & Technology, Dehradun, IN
Source
Indian Journal of Bioinformatics and Biotechnology, Vol 2, No 5 (2013), Pagination: 88-94Abstract
Protein sequence of Plasmodium yoelii yoelii "prt_seq No definition line found" was extracted from GenPept database (ACCESSION: EAA21357), used to predict its hydrophobic, atomic and amino acid composition, PEST region, solvent accessibility, molecular mass, theoretical pI and finally catalytic site detail was identified with their three dimensional structure. Analysis was made using several bioinformatics tool. PEST region was indentified using pestfind tool, whose abundant availability indicates intracellular half-lives of less than two hour. Hydrophobicity was checked using [1] to know it's buried or exposed state in terms of solvent accessibility, also used to find its different physical and chemical properties, secondary structure composition using Hidden Markov models, formation of disulphide bond, effect of point mutation prediction using heat map representation and finally catalytic site identification were made. Online Active site prediction was made using web server [2], where given protein sequence was matched with server's library of catalytic site, resulting in twenty six identified region with maximum score of 0.015 with Orotidine "5-monophosphate decarboxylase" and minimum score of 0.004 with "Endo-alpha-sialidase". Molecular weight of retrieved protein sequence was found to be 32049.9 and Theoretical Pi value was 6.08, protein close to given Pi and molecular mass was matched using TagIdent web server [3], which reveal 126466 protein. The Instability Index was computed to be 36.19 which classifies the protein as stable and the Aliphatic Index showing relative value occupied by aliphatic side chain (alanine, valine, isoleucine, and leucine) was 80.77. The three dimensional structure of catalytic site was visualized using Jmol software.Keywords
Catalytic Site, Heatmap Representation, Propsearch, Solvent Accessibility, PEST RegionReferences
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