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هفتمین همایش بیو انفورماتیک ایران
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| عنوان فارسی |
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| چکیده فارسی مقاله |
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| کلیدواژه‌های فارسی مقاله |
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| عنوان انگلیسی |
Calculation and user-friendly reporting of anticipated amplicons from (un)specific primer-binding on bisulfite-treated genomes |
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| چکیده انگلیسی مقاله |
DNA methylation is an epigenetic mechanism of gene regulation. Most wet-lab DNA methylation analyses are based on bisulfite-treated DNA. Bisulfite treatment of DNA converts unmethylated cytosine nucleotides to uracil, while sparing methylated cytosines [1]. Although searching against modified genome is an important step in primer design, NCBI primer blast does not support searching against bisulfite-treated genomes [2]. This search is essential for designing acceptable methylation specific-primers and bisulfite sequencing primers. We developed an R script that takes 2 or more primers, searches unmodified genome and bisulfite modified genome for exact and non-exact matches and returns a tabulated excel file containing the possible amplicons. The information given are: 1- Length of the resulting amplicon with primers 2-Number of mismatches to the left and right primers, 3-, and a visual guide to the places of mismatches of primers. |
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| کلیدواژه‌های انگلیسی مقاله |
primer, mismatch, bisulfite-treated genome, R script |
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| نویسندگان مقاله |
Seyed Ahmad Salehzadeh - Tarbiat Modares University, Tehran
Ali Mohammadian - Tarbiat Modares University, Tehran
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| نشانی اینترنتی |
www.icb7.ir |
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دریافت فایل مقاله |
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| زبان مقاله منتشر شده |
en |
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