Removing Gapped Columns From A Multiple Sequence Alignment.

Question

[microbeatic]

Hello,

I was wondering if there is a way in Biopython to remove columns from multiple sequence alignment that have gaps.

There is a whole section here on manipulating alignments but there is no function that deals with gaps.

My intentions are to remove columns that have gaps of any size, one or all.

Any help will be great.

Thank you

Something similar to what this program does.

[5heikki]

Since gaps are marked by a specific symbol like "-" or ".", shouldn't this be rather trivial to achieve? It's not necessarily a very good idea though..

[sammy.ich17]

Hi, I have bit similar problem. But I want to remove all the columns where any of the character is 'X'.

Answer 1

[Andreas]

Hi,

I don't think there is a specific Biopython function for this, but you could use the function prune_aln(aln, what='any_gap') in https://github.com/andreaswilm/compbio-utils/blob/master/prune_aln_cols.py where aln is for example created by AlignIO.read().

Just in case: if you are planning to run the program as such, you will also have to download https://github.com/andreaswilm/compbio-utils/blob/master/bioutils.py.

Andreas

Answer 2

[Prakki Rama]

without re-inventing the wheel, trimal does the best job in regards to this.

trimal -in test -out test_nogaps_trimal -nogaps

Answer 3

[Asaf]

You can create a set of columns that contain a gap using iterative find() over each sequence and then choose the columns not in the set.