How to conduct MOTHUR analysis of diatom (rbcL) sequence data ?

Commands in mothur
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I am trying to analyse “Novaseq” data of marine diatom. First, I need to align my sequences to a reference database using MOTHUR. However, I could not find the reference database file (alignment file) of diatom sequences. Basically I am looking for the alignment file (fasta), template file (fasta) and the taxonomy file (tax) as required for running the align.seqs and classify.seqs commands. Please suggest how to proceed with MOTHUR analysis of my diatom rbcL sequences or if someone could share these files with me.

Thanks

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Hi Adrian,

You would need to cme up with your own rbcL reference files to do the alignment and classification steps. Sorry, but I don’t know of anything prepackaged to do that. You’ll have to make it on your own using the 16S rRNA gene sequence references as a model.

Pat

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Thanks in advance, Pat. I’ll try it.

Ardian

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