Non A T G C base in RefSeq zebrafish mRNA sequence

[xiangwulu]

I found some non A T C G base in refseq zebrafish mRNA sequence:
'Y', 'K', 'R', 'M', 'W'

couldn't find out what do they mean.

e.g.
NM_001012366.1

http://www.ncbi.nlm.nih.gov/nuccore/59933235?report=fasta

at line:
CCCCCACAGTCCCTGCATTACGGGAATGTGCAGGCAAGAGGAAGCGGTCTCAGGGAGAGGAGGMCGAAGG

this is causing error for some alignment tool, such as bfast.

Thanks.

[GenoMax]

Look at IUPAC codes for degenerate nucleotides: https://en.wikipedia.org/wiki/Nucleic_acid_notation

[xiangwulu]

thanks very much.

[Brian Bushnell]

You can use Reformat with the iupacton flag to turn non-ACGT symbols to N, like this:

reformat.sh in=mrna.fasta out=reformatted.fasta iupacton