test of MAST 4-24-13

2014-08-29

azim58 - 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&amp;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"

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