Transcriptome Analysis of Spermophilus lateralis and Spermophilus tridecemlineatus Liver Does Not Suggest the Presence of Spermophilus-Liver-Specific Reference Genes

Algorithm 1

Python codes for overlap analysis by bootstrapping.

import random

from sets import Set

population = <total list of probes, n = 12575>

sample_size = 1258

def sample_wr(population, k):

# Chooses k random elements (with replacement) from a population

 # From http://code.activestate.com/recipes/273085

 n = len(population)

 _random, _int = random.random, int

 result = [None] * k

 for i in xrange(k):

  j = _int(_random() * n)

  result[i] = population[j]

 return result

distribution = range(2000)

for x in range(2000):

 sample1 = Set(sample_wr(population, sample_size))

 sample2 = Set(sample_wr(population, sample_size))

 intersect = sample1.intersection(sample2)

 distribution[x] = float(len(intersect)) / float(len(sample1))

mean = sum(distribution) / len(distribution)

variance = sum([(x − mean)**2 for x in distribution]) / len(distribution)

print ‘Population size: ’, len(population)

Print

print ‘Bootstrap distribution: ’, distribution

print ‘Bootstrap cycles: ’, len(distribution)

Print

print ‘Bootstrap mean: ’, str(mean)

print ‘Bootstrap standard deviation: ’, str(variance**0.5)