scholarly journals SNP-E: A New Method For Multiple Sequence Alignments Anal- ysis And Accurate Single Nucleotide Polymorphism Evaluation

2014 ◽  
Vol 3 (1) ◽  
pp. 206-2011
Author(s):  
Melody N. Hemmati-Sholeh ◽  
Larry A. Sholeh ◽  
David A. Lightfoot
Keyword(s):  
Single Nucleotide Polymorphism ◽  
New Method ◽  
Nucleotide Polymorphism ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Single Nucleotide ◽  
Multiple Sequence Alignments ◽  
Anal Ysis

A new method for detecting single nucleotide polymorphism using GFP-display

2004 ◽  
Vol 60 (1) ◽  
pp. 61-67 ◽  
Author(s):  
Takashi Aoki ◽  
Keiko Satoh ◽  
Tomoko Imamura ◽  
Hiroyuki Watabe
Keyword(s):  
Single Nucleotide Polymorphism ◽  
New Method ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

scholarly journals SNP-E: A New Method For Multiple Sequence Alignments Analysis And Accurate Single Nucleotide Polymorphism Evaluation

2017 ◽  
Vol 3 (1) ◽  
pp. 206-211
Author(s):  
Melody N. Hemmati-Sholeh ◽  
Larry A. Sholeh ◽  
David A. Lightfoot
Keyword(s):  
Computational Method ◽  
Genomic Research ◽  
Nucleotide Polymorphisms ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Single Nucleotide ◽  
Multiple Sequence Alignments ◽  
Microsoft Office ◽  
Change Identification ◽  
Identification Analysis

Identification of single nucleotide polymorphisms (SNPs) and insertion-deletion mutations are important for discovering the connection between the genetic mutations and complex diseases. The objective of this study was to develop a sensitive and accurate computational method for SNP detection among Multiple Sequence Alignments (MSAs) to be run on Microsoft Office SuiteTM and WindowsTM. The SNP-Evaluator, was designed to simulate the process of human eye visual change-identification. Analysis of three 82-Kbp genomic loci derived from Sanger sequencing and the corresponding SNPs from 31 genomes from IlluminaTM sequencing of soybean (Glycine max L. Merr.) demonstrated that the SNP-E was an effective method for medium-scale genomic research.

scholarly journals Analisis Single Nucleotide Polymorphism Gen Faktor Transkripsi MYB dalam Biosintesis Antosianin Kulit Buah Mangga (Analysis of Single Nucleotide Polymorphism Gene Transcription Factor MYB in Mango Skin Anthocyanin Biosynthesis)

2021 ◽  
Vol 31 (1) ◽  
pp. 1
Author(s):  
Findy Ashgi ◽  
Adi Pancoro
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Transcription Factor ◽  
Skin Color ◽  
Stop Codon ◽  
Myb Transcription Factor ◽  
Nucleotide Polymorphism ◽  
Multiple Sequence ◽  
Single Nucleotide ◽  
Fruit Skin ◽  
Transcription Factor Genes

<p>Perkembangan pasar bebas berdampak terhadap selera produk-produk pertanian, seperti warna buah mangga. Antosianin merupakan senyawa yang bertanggung jawab dalam menginduksi warna pada buah. Senyawa ini diregulasi oleh gen faktor transkripsi MYB. Mutasi Single Nucleotide Polymorphism (SNP) daerah ekson gen MYB dapat mengubah asam amino yang memengaruhi aktivitas enzim yang mengakibatkan munculnya variasi fenotipe warna buah di antara individu-individu dalam spesies yang sama. Penelitian ini bertujuan menemukan SNP pada gen MYB dari kulit buah mangga varietas Arum Manis, Gedong Gincu, Manalagi, Golek, dan Cengkir. Penelitian dilakukan dengan tiga tahap utama, yaitu isolasi DNA kulit buah mangga, Polymerase Chain Reaction (PCR), dan proses sekuensing oleh Macrogen Inc. (Singapore). Hasil multiple sequence alignment asam amino gen faktor transkripsi MYB menunjukkan adanya perbedaan basa yang mengakibatkan munculnya stop codon dari SNP 337 A→T dan SNP 338 A→G yang memengaruhi fenotipe warna kulit buah. SNP yang memunculkan stop codon dapat direkomendasikan untuk membedakan fenotipe pigmentasi antosianin pada kulit buah mangga Gedong Gincu yang bewarna merah dengan warna kulit buah mangga yang lainnya. Adanya SNP menyebabkan prematur stop codon yang terjadi pada gen faktor transkripsi MYB dan diduga berpengaruh terhadap pigmentasi antosianin.</p><p><strong>Keywords</strong></p><p>Mangga; SNP; Faktor transkripsi; Antosianin; MYB</p><p><strong>Abstract </strong></p><p>The development of free markets gives an impact on appetite for agricultural products, such as the color of mangoes fruit skin. Anthocyanins are compounds that are responsible for giving color to the fruit skin, these compounds are regulated by the MYB transcription factor genes. Single Nucleotide Polymorphism (SNP) mutations in the exon region of the MYB gene can change amino acids that affect enzyme activity, resulting in phenotypic variations in fruit color among individuals in the same species. This study aims to find SNP in MYB genes from mango peel varieties Arum Manis, Gedong Gincu, Manalagi, Golek, and Cengkir. The research was conducted in three main stages, namely isolation of mango peel DNA, Polymerase Chain Reaction (PCR), and sequencing process by Macrogen Inc (Singapore). The results of multiple sequence alignment of the amino acid MYB transcription factor genes showed a base difference which resulted in the appearance of a stop codon from SNP 337 A→T and SNP 338 A→G which affected the phenotype of fruit skin color. The SNP that raises the stop codon can be recommended to differentiate the anthocyanin pigmentation phenotype on the red skin of the mango Gedong Gincu from the skin color of other mangoes. The presence of SNP causes premature stop codon that occurs in the MYB transcription factor gene and is thought to have an effect on anthocyanin pigmentation.</p><p> </p>

scholarly journals Boosting alignment accuracy through adaptive local realignment

2016 ◽  
Author(s):  
Dan DeBlasio ◽  
John Kececioglu
Keyword(s):  
New Method ◽  
Alignment Accuracy ◽  
Global Alignment ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Local Realignment ◽  
First Time ◽  
Final Alignment

AbstractMotivationWhile mutation rates can vary across the residues of a protein, when computing alignments of protein sequences the same setting of values for substitution score and gap penalty parameters is typically used across their entire length. We provide for the first time a new method called adaptive local realignment that automatically uses diverse parameter settings in different regions of the input sequences when computing multiple sequence alignments. This allows parameter settings to adapt to more closely match the local mutation rate across a protein.MethodOur method builds on our prior work on global alignment parameter advising with the Facet alignment accuracy estimator. Given a computed alignment, in each region that has low estimated accuracy, a collection of candidate realignments is generated using a precomputed set of alternate parameter settings. If one of these alternate realignments has higher estimated accuracy than the original subalignment, the region is replaced with the new realignment, and the concatenation of these realigned regions forms the final alignment that is output.ResultsAdaptive local realignment significantly improves the quality of alignments over using the single best default parameter setting. In particular, this new method of local advising, when combined with prior methods for global advising, boosts alignment accuracy by as much as 26% over the best default setting on hard-to-align benchmarks (and by 6.4% over using global advising alone).AvailabilityA new version of the Opal multiple sequence aligner that incorporates adaptive local realignment using Facet for parameter advising, is available free for non-commercial use at http://[email protected]

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