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
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.hiv.lanl.gov/content/sequence/TRANSLATE/translate.html