scholarly journals In SilicoExpressed Sequence Tag Analysis in Identification of Probable Diabetic Genes as Virtual Therapeutic Targets

2013 ◽  
Vol 2013 ◽  
pp. 1-9
Author(s):  
Pabitra Mohan Behera ◽  
Deepak Kumar Behera ◽  
Aparajeya Panda ◽  
Anshuman Dixit ◽  
Payodhar Padhi
Keyword(s):  
Expressed Sequence Tags ◽  
Therapeutic Targets ◽  
Gene Products ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Putative Gene ◽  
Est Analysis ◽  
Treatment Of Diabetes ◽  
Conceptual Translation ◽  
Expressed Sequence

The expressed sequence tags (ESTs) are major entities for gene discovery, molecular transcripts, and single nucleotide polymorphism (SNPs) analysis as well as functional annotation of putative gene products. In our quest for identification of novel diabetic genes as virtual targets for type II diabetes, we searched various publicly available databases and found 7 reported genes. Thein silicoEST analysis of these reported genes produced 6 consensus contigs which illustrated some good matches to a number of chromosomes of the human genome. Again the conceptual translation of these contigs produced 3 protein sequences. The functional and structural annotations of these proteins revealed some important features which may lead to the discovery of novel therapeutic targets for the treatment of diabetes.

Survey of a cDNA library from the turkey (Meleagris gallopavo)

Genome ◽  
2005 ◽  
Vol 48 (1) ◽  
pp. 12-17 ◽  
Author(s):  
L D Chaves ◽  
J A Rowe ◽  
K M Reed
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Expressed Sequence Tags ◽  
Expressed Sequence Tag ◽  
Meleagris Gallopavo ◽  
Whole Genome Sequence ◽  
Snp Discovery ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Important Species ◽  
Expressed Sequence

Genome characterization and analysis is an imperative step in identifying and selectively breeding for improved traits of agriculturally important species. Expressed sequence tags (ESTs) represent a transcribed portion of the genome and are an effective way to identify genes within a species. Downstream applications of EST projects include DNA microarray construction and interspecies comparisons. In this study, 694 ESTs were sequenced and analyzed from a library derived from a 24-day-old turkey embryo. The 437 unique sequences identified were divided into 76 assembled contigs and 361 singletons. The majority of significant comparative matches occurred between the turkey sequences and sequences reported from the chicken. Whole genome sequence from the chicken was used to identify potential exon–intron boundaries for selected turkey clones and intron-amplifying primers were developed for sequence analysis and single nucleotide polymorphism (SNP) discovery. Identified SNPs were genotyped for linkage analysis on two turkey reference populations. This study significantly increases the number of EST sequences available for the turkey.Key words: turkey, cDNA, expressed sequence tag, single nucleotide polymorphism.

scholarly journals Identification of single nucleotide polymorphism in ginger using expressed sequence tags

2009 ◽  
Vol 4 (3) ◽  
pp. 119-122 ◽  
Author(s):  
Arumugam Chandrasekar ◽  
Aikkal Riju ◽  
Kandiyl Sithara ◽  
Sahadevan Anoop ◽  
Santhosh J Eapen
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Expressed Sequence Tags ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Expressed Sequence

scholarly journals Mining for Single Nucleotide Polymorphisms in Expressed Sequence Tags of European Sea Bass

2007 ◽  
Vol 4 (3) ◽  
pp. 158-167 ◽  
Author(s):  
E. L. Souche ◽  
B. Hellemans ◽  
J. K. J. Van Houdt ◽  
A. Canario ◽  
S. Klages ◽  
...  
Keyword(s):  
Positive Predictive Value ◽  
Expressed Sequence Tags ◽  
Predictive Value ◽  
In Silico ◽  
Sea Bass ◽  
Candidate Snps ◽  
Snp Discovery ◽  
European Sea Bass ◽  
Single Nucleotide ◽  
Expressed Sequence

Abstract As a multitude of sequence data are published, discovering polymorphisms bioinformatically becomes a valid option. In silico Single Nucleotide Polymorphism (SNP) detection is based on the analysis of multiple alignments. Each column of an alignment is considered a slice containing one base of every sequence aligned. If a mismatch is detected, the slice is further analysed and the mismatch may be reported as a candidate SNP.About 30,000 Expressed Sequence Tags (ESTs) of the fish European sea bass have been sequenced and processed. Since ESTs are redundant, they provide a resource for in silico SNP discovery. To prevent the detection of sequencing errors, a redundancy of two is chosen in order for a mismatch to be considered a candidate SNP. Among the various tools available to detect candidate SNPs, three software packages were tested: SNPServer, PolyBayes and PolyFreq. Candidate SNPs were validated in the laboratory by cloning and sequencing. From preliminary results PolyFreq outperforms both PolyBayes and SNPServer in terms of positive predictive value and SNPServer is the most sensitive tool. PolyFreq and SNPServer non-default identify respectively the fewest and highest number of candidates. Considering candidates detected by several tools seems to enhance both positive predictive value and sensitivity. Out of the 69 loci sequenced, only four were monomorphic, leading to a total of 91.3% polymorphic loci. Randomly chosen contigs will be sequenced to know whether SNP discovery tools tend to predict polymorphic fragments. Polymorphisms will be mapped, used for selection in aquaculture and the study of adaptation in natural populations.

Population structure of pigs determined by single nucleotide polymorphisms observed in assembled expressed sequence tags

2011 ◽  
Vol 83 (1) ◽  
pp. 14-22 ◽  
Author(s):  
Toshimi MATSUMOTO ◽  
Naohiko OKUMURA ◽  
Hirohide UENISHI ◽  
Takeshi HAYASHI ◽  
Noriyuki HAMASIMA ◽  
...  
Keyword(s):  
Population Structure ◽  
Single Nucleotide Polymorphisms ◽  
Expressed Sequence Tags ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Expressed Sequence
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