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Old 09-16-2015, 10:19 AM   #1
prepagam
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Location: N.California

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Default problem '.' characters in multiple alignment format (MAF)

Hi
I recently downloaded the Compara.39_eutherian_mammals_EPO_LOW_COVERAGE.chr* maf (Multiple alignment format) files from ensembl.
I'm trying to process the files, and some of the software I'm trying to use (e.g. mafTools) is having issues with the files because the nucleotide sequence has '.' in it.
e.g. "AGTTCAACTCTC----TTAGAACAGTCTCACTGTGTGTGAACCAATATTGCAAGAAATCACACTCAGAAAACCCATTGCTGCAGAGTCAATTGG........" (NB. the '.' at the end are the '.' i'm talking about)

I'm a bit confused because I was expecting only nucleotides, or '-' or 'N'.
There are N's in the file so it doesnt make sense that '.' means missing.
Does anyone know what the '.' means?

Thanks in advance
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