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Old 10-22-2014, 07:33 AM   #1
Alex Clop
Location: London

Join Date: Sep 2008
Posts: 15
Default TargetScan input files

Hi there,

I want to identify conserved miRNA target sites in the pig (Sus scrofa) using TargetScan. This tool requires (i) a list of miRNAs and (ii) a list of aligned 3'UTR sequences from many species (multiple sequence alignments - MSA).

The list of miRNAs contains: miRNA_family, species, seed.
The MSA file contains: gene_name, species, sequence.

Both files require matching species information.

I am a bit confused by this requirement. My MSA file contains the sequences from 5 mammalian species. Many of the miRNAs I have selected are from other species including the chicken (which was not used to obtain the MSA file) and therefore the species information in my two files does not match. Can I cheat and modify the species source in the miRNA file (replace chicken by pig)?

Also, I realise that for some of the miRNAs not identified in the pig are actually present (and expressed) but have a different seed sequence (differ in 1 nucleotide position). Again, can I cheat and modify the seed sequence in the input miRNA file?

Thanks for your comments and help.

Best regards!

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