Imputing missing data in aligned sequences

Posted by Kwame Oduro on Stack Overflow See other posts from Stack Overflow or by Kwame Oduro
Published on 2012-09-06T15:31:07Z Indexed on 2012/09/06 15:38 UTC
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perl

I want a simple perl script that can help me impute missing nucleotides in aligned sequences: As an example, my old_file contains the following aligned sequences:

seq1
ATGTC
seq2
ATGTC
seq3
ATNNC
seq4
NNGTN
seq5
CTCTN

So I now want to infer all Ns in the file and get a new file with all the Ns inferred based on the majority nucleotide at a particular position. My new_file should look like this:

seq1
ATGTC
seq2
ATGTC
seq3
ATGTC
seq4
ATGTC
seq5
CTCTC

A script with usage: "impute_missing_data.pl old_file new_file" or any other approach will be helpful to me. Thank you.

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Imputing missing data in aligned sequences - Developer IT

Imputing missing data in aligned sequences

perl

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