# question 8
util.searchAndSave("P08684", p08684_filename)
util.searchAndSave("Q16802", q16802_filename)
matrix_names = ["blosum62.matrix", "p450.matrix"]
# list of matrices though which we shall iterate to obtain various alignments
matrices = []
for matrix_name in matrix_names:
matrix = readSubstMatrix(matrix_name, Protein_Alphabet)
print "Adding matrix: " + matrix_name + "\n", matrix
matrices.append(matrix)
# read our residue sequences from FASTAs
P08684 = readFastaFile(p08684_filename)[0]
Q16802 = readFastaFile(q16802_filename)[0]
local_alignments = AlignmentCollection("question 10 local")
global_alignments = AlignmentCollection("question 10 global")
for matrix in matrices:
print "processing matrix:", matrix.name
for gap_penalty in range(-1, -20, -1):
local_alignments.add_alignment(alignLocal(P08684, Q16802, matrix, gap_penalty))
global_alignments.add_alignment(alignGlobal(P08684, Q16802, matrix, gap_penalty))
local_alignments.dump_xml_and_html("question_10_local_alignments")
global_alignments.dump_xml_and_html("question_10_global_alignments")
from sequence import *
from alignments import AlignmentCollection, AlignmentThread
HQ659871_1 = getSequence("HQ659871.1", "genbank")
JX416721_1 = getSequence("JX416721.1", "genbank")
matrix_names = ["dna.matrix", "dna.matrix4", "dna.matrix.unknown"]
# list of matrices though which we shall iterate to obtain various alignments
matrices = []
for matrix_name in matrix_names:
matrix = readSubstMatrix(matrix_name, DNA_Alphabet)
print "Adding matrix: " + matrix_name + "\n", matrix
matrices.append(matrix)
local_alignments = AlignmentCollection("question 7 local")
global_alignments = AlignmentCollection("question 7 global")
print "number of cells in alignment matrix = ", len(HQ659871_1) * len(JX416721_1)
threads = []
print "HQ659871_1 = ", len(HQ659871_1)
print "JX416721_1 = ", len(JX416721_1)
for matrix in matrices:
print "processing matrix:", matrix.name
for gap_penalty in range(-1, -20, -1):
local_alignments.add_alignment(alignLocal(HQ659871_1, JX416721_1, matrix, gap_penalty))
global_alignments.add_alignment(alignGlobal(HQ659871_1, JX416721_1, matrix, gap_penalty))