Home News Feed

search engine by freefind	advanced

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?

About Edit