核苷酸和氨基酸蛋白序列转换的工具

时间：2024-02-29 11:06:31

 

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

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