예제 #1
0
print IUPACData.ambiguous_dna_complement	#dictionary of complements
#and a lot more
from Bio.Data import CodonTable
print CodonTable.generic_by_id[2]

#SeqUtils. Several functions to deal with DNA and protein sequences.
#DNA utils
import Bio.SeqUtils as SeqUtils
print SeqUtils.GC('gacgatcggtattcgtag')	#GC content
from Bio.SeqUtils import MeltingTemp
print MeltingTemp.Tm_staluc('tgcagtacgtatcgt')	#DNA/RNA melting temperature
#checksum functions: short alphanumeric string signature of a file or sequence
#usually written in description of sequence
#cgc is a easy, weak, very used checksum (better crc32, crc64)
from Bio.SeqUtils import CheckSum
myseq='acaagatgccattgtcccccggcctcctgctgctgct'
print CheckSum.gcg(myseq)
print CheckSum.crc32(myseq)
print CheckSum.crc64(myseq)
print CheckSum.seguid(myseq)
#Protein utils
from Bio.SeqUtils import ProtParam
myprot=ProtParam.ProteinAnalysis('MLTNK')
print myprot.count_amino_acids()
print myprot.get_amino_acids_percent()
print myprot.molecular_weight()
print myprot.aromaticity()
print myprot.instability_index()
print myprot.flexibility()
print myprot.isoelectric_point()
print myprot.secondary_structure_fraction()