p53_inhouse/lambda_pcr.R at master · rtmag/p53_inhouse · GitHub

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library(stringr)
library("Biostrings")

s = readDNAStringSet("fetch-sequences_soap.py")

x=letterFrequencyInSlidingView(s[[1]],letters=c("C","G"),view.width=c(1000))

x = rowSums(x)

tail(sort(x),5)

substr(as.character(s[[1]]), start = 9903, stop = 10903)

> 4180 - 5180
GGCTCCGGTCGTATGGCCATCGATGGTCTGAAAGAAGTTCAGGAAGCGGTGATGCTGATAGAAGCCGGACTGAGTACCTACGAGAAAGAGTGCGCAAAACGCGGTGACGACTATCAGGAAATTTTTGCCCAGCAGGTCCGTGAAACGATGGAGCGCCGTGCAGCCGGTCTTAAACCGCCCGCCTGGGCGGCTGCAGCATTTGAATCCGGGCTGCGACAATCAACAGAGGAGGAGAAGAGTGACAGCAGAGCTGCGTAATCTCCCGCATATTGCCAGCATGGCCTTTAATGAGCCGCTGATGCTTGAACCCGCCTATGCGCGGGTTTTCTTTTGTGCGCTTGCAGGCCAGCTTGGGATCAGCAGCCTGACGGATGCGGTGTCCGGCGACAGCCTGACTGCCCAGGAGGCACTCGCGACGCTGGCATTATCCGGTGATGATGACGGACCACGACAGGCCCGCAGTTATCAGGTCATGAACGGCATCGCCGTGCTGCCGGTGTCCGGCACGCTGGTCAGCCGGACGCGGGCGCTGCAGCCGTACTCGGGGATGACCGGTTACAACGGCATTATCGCCCGTCTGCAACAGGCTGCCAGCGATCCGATGGTGGACGGCATTCTGCTCGATATGGACACGCCCGGCGGGATGGTGGCGGGGGCATTTGACTGCGCTGACATCATCGCCCGTGTGCGTGACATAAAACCGGTATGGGCGCTTGCCAACGACATGAACTGCAGTGCAGGTCAGTTGCTTGCCAGTGCCGCCTCCCGGCGTCTGGTCACGCAGACCGCCCGGACAGGCTCCATCGGCGTCATGATGGCTCACAGTAATTACGGTGCTGCGCTGGAGAAACAGGGTGTGGAAATCACGCTGATTTACAGCGGCAGCCATAAGGTGGATGGCAACCCCTACAGCCATCTTCCGGATGACGTCCGGGAGACACTGCAGTCCCGGATGGACGCAACCCGCCAGATGTTTGCGCAGAAGGTGTCGGCATATACCG

> 9903 - 10903
TGGCATAACCATCCGCAGAAGACGCAGATGCCGTCCATGAATGAAGCCGTTAAACAGATTGAGCAGGAAGTGCTTACCACCTGGCCCACGGAGGCAATTTCTCATGCTGAAAACGTGGTGTACCGGCTGTCTGGTATGTATGAGTTTGTGGTGAATAATGCCCCTGAACAGACAGAGGACGCCGGGCCCGCAGAGCCTGTTTCTGCGGGAAAGTGTTCGACGGTGAGCTGAGTTTTGCCCTGAAACTGGCGCGTGAGATGGGGCGACCCGACTGGCGTGCCATGCTTGCCGGGATGTCATCCACGGAGTATGCCGACTGGCACCGCTTTTACAGTACCCATTATTTTCATGATGTTCTGCTGGATATGCACTTTTCCGGGCTGACGTACACCGTGCTCAGCCTGTTTTTCAGCGATCCGGATATGCATCCGCTGGATTTCAGTCTGCTGAACCGGCGCGAGGCTGACGAAGAGCCTGAAGATGATGTGCTGATGCAGAAAGCGGCAGGGCTTGCCGGAGGTGTCCGCTTTGGCCCGGACGGGAATGAAGTTATCCCCGCTTCCCCGGATGTGGCGGACATGACGGAGGATGACGTAATGCTGATGACAGTATCAGAAGGGATCGCAGGAGGAGTCCGGTATGGCTGAACCGGTAGGCGATCTGGTCGTTGATTTGAGTCTGGATGCGGCCAGATTTGACGAGCAGATGGCCAGAGTCAGGCGTCATTTTTCTGGTACGGAAAGTGATGCGAAAAAAACAGCGGCAGTCGTTGAACAGTCGCTGAGCCGACAGGCGCTGGCTGCACAGAAAGCGGGGATTTCCGTCGGGCAGTATAAAGCCGCCATGCGTATGCTGCCTGCACAGTTCACCGACGTGGCCACGCAGCTTGCAGGCGGGCAAAGTCCGTGGCTGATCCTGCTGCAACAGGGGGGGCAGGTGAAGGACTCCTTCGGCGGGATGATCCCCATGTTCAGGGGGCTTGCCGGTGCGATCACCCTGCC