R语言Biostrings包函数介绍（一）

最新推荐文章于 2023-08-31 06:30:00 发布

零级伪码农

最新推荐文章于 2023-08-31 06:30:00 发布

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本文介绍了R语言Biostrings包的主要功能，包括定义的常量、单一序列类、XStringViews类、序列集类以及基本的序列转换操作，如DNA到RNA的转录和互补配对。通过示例展示了如何创建和操作BString、DNAString等对象，以及进行序列比对和转换的方法。

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一、定义的常量

> DNA_BASES 
[1] "A" "C" "G" "T"
> RNA_BASES 
[1] "A" "C" "G" "U"
> GENETIC_CODE 
TTT TTC TTA TTG TCT TCC TCA TCG TAT TAC TAA TAG TGT TGC TGA TGG CTT 
"F" "F" "L" "L" "S" "S" "S" "S" "Y" "Y" "*" "*" "C" "C" "*" "W" "L" 
CTC CTA CTG CCT CCC CCA CCG CAT CAC CAA CAG CGT CGC CGA CGG ATT ATC 
"L" "L" "L" "P" "P" "P" "P" "H" "H" "Q" "Q" "R" "R" "R" "R" "I" "I" 
ATA ATG ACT ACC ACA ACG AAT AAC AAA AAG AGT AGC AGA AGG GTT GTC GTA 
"I" "M" "T" "T" "T" "T" "N" "N" "K" "K" "S" "S" "R" "R" "V" "V" "V" 
GTG GCT GCC GCA GCG GAT GAC GAA GAG GGT GGC GGA GGG 
"V" "A" "A" "A" "A" "D" "D" "E" "E" "G" "G" "G" "G" 
attr(,"alt_init_codons")
[1] "TTG" "CTG"
> RNA_GENETIC_CODE
UUU UUC UUA UUG UCU UCC UCA UCG UAU UAC UAA UAG UGU UGC UGA UGG CUU 
"F" "F" "L" "L" "S" "S" "S" "S" "Y" "Y" "*" "*" "C" "C" "*" "W" "L" 
CUC CUA CUG CCU CCC CCA CCG CAU CAC CAA CAG CGU CGC CGA CGG AUU AUC 
"L" "L" "L" "P" "P" "P" "P" "H" "H" "Q" "Q" "R" "R" "R" "R" "I" "I" 
AUA AUG ACU ACC ACA ACG AAU AAC AAA AAG AGU AGC AGA AGG GUU GUC GUA 
"I" "M" "T" "T" "T" "T" "N" "N" "K" "K" "S" "S" "R" "R" "V" "V" "V" 
GUG GCU GCC GCA GCG GAU GAC GAA GAG GGU GGC GGA GGG 
"V" "A" "A" "A" "A" "D" "D" "E" "E" "G" "G" "G" "G" 
attr(,"alt_init_codons")
[1] "UUG" "CUG"
> AMINO_ACID_CODE
    A     R     N     D     C     Q     E     G     H     I     L 
"Ala" "Arg" "Asn" "Asp" "Cys" "Gln" "Glu" "Gly" "His" "Ile" "Leu" 
    K     M     F     P     S     T     W     Y     V     U     O 
"Lys" "Met" "Phe" "Pro" "Ser" "Thr" "Trp" "Tyr" "Val" "Sec" "Pyl" 
    B     J     Z     X 
"Asx" "Xle" "Glx" "Xaa" 
> IUPAC_CODE_MAP
     A      C      G      T      M      R      W      S      Y      K 
   "A"    "C"    "G"    "T"   "AC"   "AG"   "AT"   "CG"   "CT"   "GT" 
     V      H      D      B      N 
 "ACG"  "ACT"  "AGT"