Script to remove gap-only sites from fasta alignment?

kmkocot · 02-15-2010, 04:21 PM

Hi all,

I am trying to find a script or a program that I can call in a pipeline that can remove gap-only sites in a multiple sequence alignment. Can you think of anything I can use? I'd also like to
delete the columns at either end of each alignment where there are only 2 or fewer sequences with non-gap characters if you can think of anything that can do that.

Thanks!
Kevin

maubp · 02-23-2010, 02:19 AM

I can picture how I would solve this using Biopython, provided the whole alignment can be loaded into RAM.

How big are the alignments (number of columns, number of rows)?

nilshomer · 02-23-2010, 09:16 AM

Quote:

Originally Posted by kmkocot

Hi all,

I am trying to find a script or a program that I can call in a pipeline that can remove gap-only sites in a multiple sequence alignment. Can you think of anything I can use? I'd also like to
delete the columns at either end of each alignment where there are only 2 or fewer sequences with non-gap characters if you can think of anything that can do that.

Thanks!
Kevin

Given your alignments in the SAM format, you can remove all alignments with indels with the C-program "dbamfilter -i". You could also easily parse the CIGAR field in the SAM format for any "I" or "D" operators.

What format are you working with?

kmkocot · 02-23-2010, 09:52 AM

Hi maubp,

The alignments vary but all have fewer than 30 taxa and fewer than 1000 amino acids.

Thanks,
Kevin

kmkocot · 02-23-2010, 10:50 AM

Hi maubp,

The alignments vary but all have fewer than 30 taxa and fewer than 1000 amino acids.

Thanks,
Kevin

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02-15-2010, 04:21 PM	#1
kmkocot Member Location: Alabama Join Date: Jun 2009 Posts: 48	Script to remove gap-only sites from fasta alignment? Hi all, I am trying to find a script or a program that I can call in a pipeline that can remove gap-only sites in a multiple sequence alignment. Can you think of anything I can use? I'd also like to delete the columns at either end of each alignment where there are only 2 or fewer sequences with non-gap characters if you can think of anything that can do that. Thanks! Kevin

02-23-2010, 02:19 AM	#2
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	I can picture how I would solve this using Biopython, provided the whole alignment can be loaded into RAM. How big are the alignments (number of columns, number of rows)?

02-23-2010, 09:52 AM	#4
kmkocot Member Location: Alabama Join Date: Jun 2009 Posts: 48	Hi maubp, The alignments vary but all have fewer than 30 taxa and fewer than 1000 amino acids. Thanks, Kevin

02-23-2010, 10:50 AM	#5
kmkocot Member Location: Alabama Join Date: Jun 2009 Posts: 48	Hi maubp, The alignments vary but all have fewer than 30 taxa and fewer than 1000 amino acids. Thanks, Kevin