test+of+MAST+4-24-13

4-24-13 I want to test out the MAST program. First I need to make a fake output meme file. I'll use the 108 SMC1fs peptides to get the template for such a file. slight change of plans

MAST requires an output xml file from meme. To make my fake xml file, I will submit 3 sequences for each sequence I'm interested in with some fake sequence surrounding it for meme to give me the motif I want. I'll randomly choose four sequences from the Cfdp1 protein.

Genbank: CAG46908.1 (homo sapiens)

-sequences

EEDEDY

EDARKKK

ANVPS

AKKQKM

IHNR

now I'll generate some fake sequences from these "F:\kurt\storage\CIM Research Folder\DR\2013\4-24-13\meme\artificial_cfdp1_motif_containing_sequences.txt"

I used MEME which correctly found the 5 motifs. output xml file here "F:\kurt\storage\CIM Research Folder\DR\2013\4-24-13\meme\artificially_produced_cfdp1_meme_output.xml"

I could not get MAST to correctly identify the Cfdp1 protein though. email thread here https://mail.google.com/mail/u/0/?ui=2&shva=1#sent/13e3d21938ae667c

Actually, the Cfdp1 protein is correctly identified if I use the Swiss Prot database. Output files here: "F:\kurt\storage\CIM Research Folder\DR\2013\4-24-13\meme\mast_cfdp1_output.html" "F:\kurt\storage\CIM Research Folder\DR\2013\4-24-13\meme\mast_cfdp1_output.xml"