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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 translatedef reverse_complement( sequence ): reversed_sequence = (sequence[::-1]) rc = ‘‘.join([basepairs.get(reversed_sequence[i], ‘X‘) for i in range(len(sequence))]) return rcprint(translate_frameshifted(beans[0:])) # first frameprint(translate_frameshifted(beans[1:])) # second frameprint(translate_frameshifted(beans[2:])) # third frameprint(translate_frameshifted(reverse_complement(beans))) # negative first frameprint(translate_frameshifted(reverse_complement(beans[:len(beans)-1]))) # negative second frameprint(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
核苷酸和氨基酸蛋白序列转换的工具
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