question details 07-18-2014d1439

2014-08-29

What happens if I use mast with the frameshift database using some of the best motifs from this evolution run: C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\07-08-2014d0933\decipher work 07-08-2014d0933\evolution with avoidance of high scoring already found motifs 07-11-2014d0950
{

First I'll try just
[TISKYVMVEPMRQHEEW, GGEKRRKNATKHEQWIL, IMLHPPWMLIQHTMWNQ, IFRYVKDFAKADTHKWM, KSHDLGNDRSMKFRNRG, KHEMWNWVFLTVNKERV]	QHEEW	43.0997	5
and
[PMWLKTYHSSWYNSSHK, HHMFMMEWMWSALHPGH, RFTWFGMWAAMFKPRPQ, KHTAFHNHETVRVHSWF, QLHHWMSSDWAGPFQHV, ESAHSLWFGWRSVRHFD]	HSSWY	40.4424	5
which were found in the top 10 best motifs

I'll use my program to create a meme file from these peptide groups.

I used this function
public void testMemeFileHandler071814()

now I can use mast with this meme file
mast smcfs_pep_groups.meme "C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\07-01-2014d1325\frameshift databases 07-01-2014d1424\version 07-13-2014d1059\Frameshift Database.fa"

SMCfs is not in the top list of matches.

What if I make the motifs artificially.

mast artificial_sg.meme "C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\07-01-2014d1325\frameshift databases 07-01-2014d1424\version 07-13-2014d1059\Frameshift Database.fa"

smcfs is also not in the list

What if I were to add the pmre?
pmrepom
pmre plus other motifs

mast pmrepom.meme "C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\07-01-2014d1325\frameshift databases 07-01-2014d1424\version 07-13-2014d1059\Frameshift Database.fa"

Wow if I add PQRE, then SMCfs is still not in the list.

What if I add PQRE?

mast pqrepom.meme "C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\07-01-2014d1325\frameshift databases 07-01-2014d1424\version 07-13-2014d1059\Frameshift Database.fa"

If I add PQRE, then SMC1A is finally in the list.

What if I do the top 10 motifs from the evolution, along with PQRE, does SMC1A show up in the list?
t10pqre

QHEEW
SHGGKW
KHEMWN
FHKMTW
HSSWY
KSHDLG
HEQWI
KHEMW
QNYTIW
HKWM

t10pqre
>1
QHEEW
>2
SHGGKW
>3
KHEMWN
>4
FHKMTW
>5
HSSWY
>6
KSHDLG
>7
HEQWI
>8
KHEMW
>9
QNYTIW
>10
HKWM
>11
PQRE
>SMC1A
CCGIYCHEEPQREDSSI

mast t10pqre.meme "C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\07-01-2014d1325\frameshift databases 07-01-2014d1424\version 07-13-2014d1059\Frameshift Database.fa"

Unfortunately, with 11 motifs which contain QHEEW and PQRE, the SMC1A sequence is not among them.

What if I use Bl2seq to align these 11 motifs with SMC1A, and I also use Bl2seq to align these 11 motifs with the best match from this mast output?
MS_Ins_CCDS13662.1|Hs104|chr21

Bl2seq t10pqre with SMC1A
Only the PQRE aligns
What about with clustal omega?
How do I get a score of an alignment in clustal omega?
}

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