核苷酸和氨基酸蛋白序列转换的工具

 

在线序列转换的工具：

Nucleotide Sequence Translation

Protein Sequence Back-translation

http://bio.lundberg.gu.se/edu/translat.html

http://www.ebi.ac.uk/Tools/st/

http://www.hiv.lanl.gov/content/sequence/TRANSLATE/translate.html

 

Python 序列转换

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beans = "TGACTGTGTTTCTGAACAATAAATGACTTAAACCAGGTATGGCTGCCGATGGTTATCTT"

 

gencode = {

      'ATA':'I', 'ATC':'I', 'ATT':'I', 'ATG':'M',

      'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACT':'T',

      'AAC':'N', 'AAT':'N', 'AAA':'K', 'AAG':'K',

      'AGC':'S', 'AGT':'S', 'AGA':'R', 'AGG':'R',

      'CTA':'L', 'CTC':'L', 'CTG':'L', 'CTT':'L',

      'CCA':'P', 'CCC':'P', 'CCG':'P', 'CCT':'P',

      'CAC':'H', 'CAT':'H', 'CAA':'Q', 'CAG':'Q',

      'CGA':'R', 'CGC':'R', 'CGG':'R', 'CGT':'R',

      'GTA':'V', 'GTC':'V', 'GTG':'V', 'GTT':'V',

      'GCA':'A', 'GCC':'A', 'GCG':'A', 'GCT':'A',

      'GAC':'D', 'GAT':'D', 'GAA':'E', 'GAG':'E',

      'GGA':'G', 'GGC':'G', 'GGG':'G', 'GGT':'G',

      'TCA':'S', 'TCC':'S', 'TCG':'S', 'TCT':'S',

      'TTC':'F', 'TTT':'F', 'TTA':'L', 'TTG':'L',

      'TAC':'Y', 'TAT':'Y', 'TAA':'_', 'TAG':'_',

      'TGC':'C', 'TGT':'C', 'TGA':'_', 'TGG':'W'}

 

basepairs = {'A':'T', 'C':'G', 'G':'C', 'T':'A'}

 

def translate_frameshifted( sequence ):

      translate = ''.join([gencode.get(sequence[3*i:3*i+3],'X') for i in range(len(sequence)//3)])

      return translate

 

def reverse_complement( sequence ):

      reversed_sequence = (sequence[::-1])

      rc = ''.join([basepairs.get(reversed_sequence[i], 'X') for i in range(len(sequence))])

      return rc

 

print(translate_frameshifted(beans[0:]))    # first frame

print(translate_frameshifted(beans[1:]))    # second frame

print(translate_frameshifted(beans[2:]))    # third frame

print(translate_frameshifted(reverse_complement(beans)))    # negative first frame

print(translate_frameshifted(reverse_complement(beans[:len(beans)-1])))    # negative second frame

print(translate_frameshifted(reverse_complement(beans[:len(beans)-2])))    # negative third frame

 

# This ::-1 syntax in python means reverse the string.

 

 

REF

https://www.biostars.org/p/55851/

http://www.soc-bdr.org/rds/authors/unit_tables_conversions_and_genetic_dictionaries/e5202/index_en.html

http://www.hiv.lanl.gov/content/sequence/TRANSLATE/translate.html