# Restricting match output for multiple sequence alignment using mafft?

So I aligned roughly 5k sequences and I got my output using mafft. However, I want to restrict the output to only present conserved segments of a specific length (let's say 25bp). Does mafft have parameters to set this that I seem to be missing?

## Q - Is there some parameter for this?

No, there is no parameter for this. Getting the conserved regions is something that you will have to perform post-alignment.

## How to get the conserved regions?

You will need to define what exactly you mean by conservation and calculate a conservation score for each position of the alignment.

For instance you can look at each column of the alignment and calculate the percent of queries that had the same base/AA at that position. If using AAs you can define conservation more loosely depending on what properties are important to you, or using a scoring matrix.

Once you have a co-occurrence matrix you can define the regions of interest based on a conservation threshold that you define.

## Is there software to find conserved columns?

There is a program MstatX which outputs conservation scores of individual columns.

## How MstatX works

The example of MstatX provides this example alignment. Each column is progressively less conserved than the last. The last column is conserved, but has some gaps -- this lowers the conservation score.

   col          1
seq1  1234567890
seq2  DDDDDDIPDL
seq3  DDDDDDIPVL
seq4  DDDDDDIPYL
seq5  DDDDDDIPA-
seq6  DDDDDDLWT-
seq7  DDEDEELWK-
seq8  DDEDEELWP-
seq9  DDEDEFVSR-
seq10 DEEFFFVSH-


The conservation scores for each column were:

1       2.71272e-08
2       0.243433
3       0.312789
4       0.243433
5       0.483364
6       0.480391
7       0.498757
8       0.498757
9       0.973514
10      0.267319


## How to get conserved regions

The python program below will output all windows of conserved regions when using a fasta alignment and the default output from MstatX.

• Positional args
• 1. MstatX_alignment_example.mali, is the fasta alignment file.
• 2. output.txt is the default output of mstatx when called with mstatx -i MstatX_alignment_example.mali.
• 3. 0.4 is the minimum conservation score
• 4. 3 is the minimum number of bases that must have that conservation score.

Calling this program with the following command on the above example:

python print_conserved_regions.py MstatX_alignment_example.mali output.txt 0.4 3 prints:

{1,4}


Meaning that there was only one window at least 3 bases long in which all positions had a conservation score below 0.4. This window was positions 1 through 4 in the alignment.

#call this file cons_windows.py
import sys
from Bio import AlignIO

align_filename = sys.argv
cons_filename = sys.argv
cutoff = float(sys.argv)
minchar = int(sys.argv)

def parse_conservation(filename):
cons = {}
with open(filename, "r") as f:
for line in f:
if line.strip():
temp = line.split()
cons[int(temp)] = float(temp)
return cons

cons = parse_conservation(sys.argv)

i = 1
while i < max(cons):
if cons[i] <= cutoff:
j = i
done = False
while j < max(cons) and not done:
if (cons[j] > cutoff) and (j-i >= minchar):
print("{{{},{}}}".format(i,j-1))
done = True
i = j
j+=1
i+=1