X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=binaries%2Fsrc%2Fdisembl%2Fbiopython-1.50%2FBio%2FSeqUtils%2FCodonUsageIndices.py;fp=binaries%2Fsrc%2Fdisembl%2Fbiopython-1.50%2FBio%2FSeqUtils%2FCodonUsageIndices.py;h=29c9756f8a1bdab0b8536be5d06f80c91afa93db;hb=f47da0247a9f9a8ac55571234064a0d3ded06b6c;hp=0000000000000000000000000000000000000000;hpb=6ff5fdd71d597d015fdc1df7eb0a352f8086eaa9;p=jabaws.git diff --git a/binaries/src/disembl/biopython-1.50/Bio/SeqUtils/CodonUsageIndices.py b/binaries/src/disembl/biopython-1.50/Bio/SeqUtils/CodonUsageIndices.py new file mode 100644 index 0000000..29c9756 --- /dev/null +++ b/binaries/src/disembl/biopython-1.50/Bio/SeqUtils/CodonUsageIndices.py @@ -0,0 +1,14 @@ +# Copyright Yair Benita Y.Benita@pharm.uu.nl +# Biopython (http://biopython.org) license applies + +# sharp Ecoli index for codon adaption index. +# from Sharp & Li, Nucleic Acids Res. 1987 +SharpEcoliIndex = { +'GCA':0.586, 'GCC':0.122, 'GCG':0.424, 'GCT':1, 'AGA':0.004, 'AGG':0.002, 'CGA':0.004, +'CGC':0.356, 'CGG':0.004, 'CGT':1, 'AAC':1, 'AAT':0.051, 'GAC':1, 'GAT':0.434, 'TGC':1, +'TGT':0.5, 'CAA':0.124, 'CAG':1, 'GAA':1, 'GAG':0.259, 'GGA':0.01, 'GGC':0.724, 'GGG':0.019, +'GGT':1, 'CAC':1, 'CAT':0.291, 'ATA':0.003, 'ATC':1, 'ATT':0.185, 'CTA':0.007, 'CTC':0.037, +'CTG':1, 'CTT':0.042, 'TTA':0.02, 'TTG':0.02, 'AAA':1, 'AAG':0.253, 'ATG':1, 'TTC':1, 'TTT':0.296, +'CCA':0.135, 'CCC':0.012, 'CCG':1, 'CCT':0.07, 'AGC':0.41, 'AGT':0.085, 'TCA':0.077, 'TCC':0.744, +'TCG':0.017, 'TCT':1, 'ACA':0.076, 'ACC':1,'ACG':0.099, 'ACT':0.965, 'TGG':1, 'TAC':1, 'TAT':0.239, +'GTA':0.495, 'GTC':0.066,'GTG':0.221, 'GTT':1}