User:James Estevez/Notebook/Spring 2011: Bdellovibrio Independent Study/2011/02/13

Bdellovibrio Independent Study

pSORTb Predictions

Average synthesis cost formula:

[math]\displaystyle{ asc=\frac{\sum \mathrm{ATP}_{aa}}{n_{aa}} }[/math]

I calculated this using a small Python script: <source lang="python">

import sys from optparse import OptionParser from Bio import SeqIO

usage = "usage: %prog fasta_file_in" parser = OptionParser(usage) parser.add_option("-i", "--input", dest="file_in", default=None,

                 help="Name of the input file")

(opts, args) = parser.parse_args() if opts.file_in:

   fh = open(opts.file_in)

elif args:

   fh = open(args[0])

elif sys.stdin:

   fh = sys.stdin

def seqcost(seq):

   cost = 0

Amino acid synthesis cost in phosphate bonds, from: Akashi, H., and T. Gojobori. 2002. Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proc Natl Acad Sci U S A 99:3695-700.

   AAcost = 	{"A":11.7,"C":24.7,"D":12.7,"E":15.3,"F":52,"G":11.7,"H":38.3,

"I":32.3,"K":30.3,"L":27.3,"M":34.3,"N":14.7,"P":20.3,"Q":16.3, "R":27.3,"S":11.7,"T":18.7,"V":23.3,"W":74.3,"Y":50}

   for aa in seq:
       cost += AAcost.get(aa,0)
   return cost

def avgcost(seq):

   for aa in seq:

ASC = seqcost(seq)/len(record.seq)

   return ASC

for record in SeqIO.parse(fh, "fasta"):

   print record.id,seqcost(record.seq),avgcost(record.seq)

</source>