I am new to python, so sorry if my question or code seems a bit weird or newbie.
I want to calculate the conservation in two sequence with a specific window size. I actually wrote the code, and it looks like this in below.
My question is, is there any shorter way of doing that using Biopython? I read their tutorial but I really couldn't find anything that I can use here. I found ways that the code tells you the overall similarity score between 2 sequences, but I want to be able check the similarity/conservation in a specific window size and eventually plot the the data.
I appreciate any suggestion/ help from you guys!
Thanks and have a nice Day
> Blockquote from Bio import AlignIO import matplotlib.pyplot as plt # Compares 2 sequences in a specific window size, and prints the difference def compare(word1, word2, window): chunk_count = 0 list =  length_word1 = len(word1) length_word2 = len(word2) if length_word1 < length_word2: min_word = word1 else: min_word = word2 while chunk_count < (len(min_word) - 1): count = 0 if chunk_count + window > len(min_word): window = len(min_word)-chunk_count for window_counter in range(window): if word1[window_counter + chunk_count] == word2[window_counter + chunk_count]: count = count + 1 list.append(count) chunk_count = chunk_count + window print(list) length= len (list) print (length) list3 =  x=0 for i in range (length-1): x= x+10 list3.append(x) print (list3) def main(): alignment = AlignIO.read("Alignment 2.aln", "clustal") word1 = (alignment.seq) word2 = (alignment.seq) window = 20 compare(word1, word2, window) > Blockquote