欧剑虹老师BOOK学习记录：第一章 R/Bioconductor入门（2):生物字符串 Biological strings

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第一章 R/Bioconductor入门

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欧剑虹老师BOOK学习记录：第一章 R/Bioconductor入门（1）

生物字符串 Biological strings

• 生物字符串的常见操作比如求互补序列，反向序列，反向互补序列，翻译，转录，逆转录，碱基频率统计，序列比对等。

# if (!requireNamespace("BiocManager", quietly = TRUE))
#    install.packages("BiocManager")
# BiocManager::install("Biostrings")
library(Biostrings) ## 加载包
dna<-DNAString("TCTCCCAACCCTTGTACCAGTATAAATCGT")

# DNA反向序列
> reverse(dna) 
  30-letter "DNAString" instance
seq: TGCTAAATATGACCATGTTCCCAACCCTCT

# DNA转换成RNA
> RNAString(dna)
  30-letter "RNAString" instance
seq: UCUCCCAACCCUUGUACCAGUAUAAAUCGU

# DNA的互补序列
> complement(dna)
  30-letter "DNAString" instance
seq: AGAGGGTTGGGAACATGGTCATATTTAGCA

# DNA反向互补序列
> reverseComplement(dna)
  30-letter "DNAString" instance
seq: ACGATTTATACTGGTACAAGGGTTGGGAGA

# DNA转录
> rna<-RNAString(complement(dna)) ## 转录，注意它与dna2rna的不同
> rna
  30-letter "RNAString" instance
seq: AGAGGGUUGGGAACAUGGUCAUAUUUAGCA
   # TCTCCCAACCCTTGTACCAGTATAAATCGT （为了方便对比，把DNA序列放在这里）
   # UCUCCCAACCCUUGUACCAGUAUAAAUCGU  （dna2rna）

# RNA转换成DNA
> DNAString(rna)
  30-letter "DNAString" instance
seq: AGAGGGTTGGGAACATGGTCATATTTAGCA

# 逆转录为cDNA
> DNAString(complement(rna)) 
  30-letter "DNAString" instance
seq: TCTCCCAACCCTTGTACCAGTATAAATCGT

# 将RNA转换成密码子
> codons(rna) 
  Views on a 30-letter RNAString subject
subject: AGAGGGUUGGGAACAUGGUCAUAUUUAGCA
views:
     start end width
 [1]     1   3     3 [AGA]
 [2]     4   6     3 [GGG]
 [3]     7   9     3 [UUG]
 [4]    10  12     3 [GGA]
 [5]    13  15     3 [ACA]
 [6]    16  18     3 [UGG]
 [7]    19  21     3 [UCA]
 [8]    22  24     3 [UAU]
 [9]    25  27     3 [UUA]
[10]    28  30     3 [GCA]

# 将密码子翻译成氨基酸
> translate(rna) 
  10-letter "AAString" instance
seq: RGLGTWSYLA

# 碱基频数的统计
> alphabetFrequency(dna)
 A  C  G  T  M  R  W  S  Y  K  V  H  D  B  N  -  +  . 
 8 10  3  9  0  0  0  0  0  0  0  0  0  0  0  0  0  0 

# 查看是否只含有四种碱基
> hasOnlyBaseLetters(dna)
[1] TRUE

# 唯一的碱基
> uniqueLetters(dna)
[1] "A" "C" "G" "T"

# 自定义统计碱基比例，如常见的CG频数
> letterFrequency(dna, letters="CG")
C|G 
 13 

# 计算GC频率
> GC_content <- letterFrequency(dna, letters="CG")/letterFrequency(dna, letters="ACGT"); GC_content
      C|G 
0.4333333 

# 搜索自定义的碱基序列
> TATA <- "TATA"
> (mT <- matchPattern(TATA, dna))
  Views on a 30-letter DNAString subject
subject: TCTCCCAACCCTTGTACCAGTATAAATCGT
views:
    start end width
[1]    21  24     4 [TATA]

# 进行序列比对
## 蛋白质序列的比对
> aa1<-AAString("HXBLVYMGCHFDCXVBEHIKQZ")
> aa2<-AAString("QRNYMYCFQCISGNEYKQN")
# 全局比对
> pairwiseAlignment(aa1, aa2, substitutionMatrix="BLOSUM62", type="global") 
Global PairwiseAlignmentsSingleSubject (1 of 1)
pattern: HXBLVYMGCHFDCXVBEHIKQZ
subject: QRN--YMYC-FQCISGNEYKQN
score: 9 
# 局部比对
> pairwiseAlignment(aa1, aa2, substitutionMatrix="BLOSUM62", type="local")
Local PairwiseAlignmentsSingleSubject (1 of 1)
pattern: [6] YMGCHFDCXVBEHIKQ
subject: [4] YMYC-FQCISGNEYKQ
score: 24 

## DNA序列的比对
> s1 <- 
+     DNAString("ACTTCACCAGCTCCCTGGCGGTAAGTTGATCAAAGGAAACGCAAAGTTTTCAAG")
> s2 <-
+     DNAString("GTTTCACTACTTCCTTTCGGGTAAGTAAATATATAAATATATAAAAATATAATTTTCATC")
## 指定罚分
> mat <- nucleotideSubstitutionMatrix(match = 1, mismatch = -3, baseOnly = TRUE)
> mat
   A  C  G  T
A  1 -3 -3 -3
C -3  1 -3 -3
G -3 -3  1 -3
T -3 -3 -3  1
> pairwiseAlignment(s1, s2, substitutionMatrix = mat,
+                       gapOpening = -5, gapExtension = -2)
Global PairwiseAlignmentsSingleSubject (1 of 1)
pattern: ACTTCACCAGCTCCCTGGCGGTAAGTTGATC---AAAGG---AAACGCAAAGTTTTCAAG
subject: GTTTCACTACTTCCTTTCGGGTAAGTAAATATATAAATATATAAAAATATAATTTTCATC
score: -52 

> pairwiseAlignment(s1, s2, type = "local", substitutionMatrix = mat,
+                       gapOpening = -5, gapExtension = -2)
Local PairwiseAlignmentsSingleSubject (1 of 1)
pattern: [20] GGTAAGT
subject: [20] GGTAAGT
score: 7

> pairwiseAlignment(s1, s2, type = "overlap", substitutionMatrix = mat,
+                       gapOpening = -5, gapExtension = -2)
Overlap PairwiseAlignmentsSingleSubject (1 of 1)
pattern: [54] G
subject:  [1] G
score: 1