MAST motif alignment and search tool 6-19-14

2015-01-13

search sequence databases with motifs

What is the difference between mast and blast?

instructions
http://meme.nbcr.net/meme/doc/mast.html

example command
{
mast <motif file> <sequence file>

./mast "C:\Users\kurtw_000\Documents\kurt\storage\lgdata_DR\2014\01-16-2014d1422\selected young aged gprs\decipher for 100 peptides by age 3 criteria\analysis of josh\glam2\output by pasting desired epitopes multiple times with no gaps.meme" "C:\Users\kurtw_000\Documents\kurt\storage\pDR\lgdata_DR\06-18-2014d1642\all human proteins\human proteins from search\sequence.fasta"
-my mast executable was located here: C:\cygwin\home\kurtw_000\meme\bin
}

command line parameters
{
-ev
print results for sequences with E-value < <ev> (default: 10)

-mt
show motif matches with p-value < mt (default: 0.0001)
--this is some kind of position e-value
--note that an mt of 1 might be a reasonable value
}

How can I perform a search with MAST using an artificial MEME motif file?
{
I think a reasonable way to do this is to edit a template meme file containing a reasonable background amino acid frequency.  Here is a template file containing amino acid frequencies from here: http://www.tiem.utk.edu/~gross/bioed/webmodules/aminoacid.htm
-"C:\Users\kurtw_000\Documents\kurt\storage\pDR\2014\06-20-2014d1406\mast resources\artificial meme file 06-20-2014d1340.meme"

Then enter the motifs.  Each motif should have a row with expected frequencies of amino acids.  I think a reasonable method for filling out the frequencies is to take the BLOSUM62 matrix values for an amino acid, and modify them for this purpose.  I modify the values so there are no negative numbers and all the values in a row add up to 1.  With this modified matrix, one can then copy and paste rows for amino acids into the motif.  For example, if the motif is NRGG, one could copy the row for N, copy the row for R, copy the row for G, and copy the row for G again.  Here is a file with the modified numbers from the BLOSUM62 matrix.
-"C:\Users\kurtw_000\Documents\kurt\storage\pDR\2014\06-20-2014d1406\mast resources\blosum62 matrix with no negatives and adjusted so rows sum to one.xlsx"
}

-use MAST to query translated pubmed est database
--e-mail and response about this here: https://mail.google.com/mail/u/0/?ui=2&shva=1#search/mast/1435a3be3f657cb2
---[transcript of email 01-07-2014d0932]

-[No scoring matrices contained any information error 06-20-2014d1410]

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