MAST of SMC1afs epitopes from random peptide array 06-25-2014d1441

2015-01-13

SMC1afs epitopes from random peptide array (also in paper with Kathy and Shen)
{
PMRQ
HEE
PMREGS
PMRE
EMPMRE
HE
}

artificial MEME file of SMC1afs epitopes (that could be produced from GLAM2)
{
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\06-25-2014d1027\SMC1afs MAST investigation\SMC1afs epitope artificial meme file 06-25-2014d1100.meme"
}

SMC1afs sequence in small unusual human peptide database
-"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\07-01-2014d1325\frameshift databases 07-01-2014d1424\Human Unusual Peptide Database.fa"
--search of database
{
mast here: C:\cygwin\home\kurtw_000\meme\bin
./mast "C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\06-25-2014d1027\SMC1afs MAST investigation\SMC1afs epitope artificial meme file 06-25-2014d1100.meme" "C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\07-01-2014d1325\frameshift databases 07-01-2014d1424\Human Unusual Peptide Database.fa"
}
---SMC1afs was the 3rd best match of all of these sequences.  Results below
----C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\07-01-2014d1325\SMC1afs mast search
--what if I search with blast: [BLAST of SMC1afs mimotopes against human unusual peptide database 07-01-2014d1640]

Human sequence in nr database that should match with SMC1fs sequence
>Accession: BC046147.1 SMC like (in the nr database). . Accesion = BC112127 on Mammalian Gene Collection website
-"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\06-26-2014d1027\smc_like.fasta"
{
>SMC_like
GCGGCCTGTCCTACTGCCGCCGGCGCCGCGGCCGTCATGGGGTTCCTGAAACTGATTGAGATTGAGAACTTTAAGTCGTACAAGGGTCGACAGATTATCGGACCATTTCAGAGGTTCACCGCCATCATTGGACCCAATGGCTCTGGGTGCTGTGGAATCTATTGCCATGAAGAACCCCAAAGAGAGGACAGCTCTATTTGAAGAGATTAGTCGTTCTGGGGAGCTGGCGCAGGAGTATGACAAGCGAAAGAAGGAAATGGTGAAGGCTGAAGAGGACACACAGTTTAATTACCATCGCAAGAAAAATATTGCGGCTGAACGCAAGGAAGCAAAGCAGGAGAAAGAAGAGGCTGACCGGTACCAGCGCCTGAAGGATGAGGTAGTACGGGCTCAGGTACAGCTGCAGCTCTTTAAGCTTTACCATAATGAAGTGGAAATTGAGAAGCTCAACAAGGAACTGGCCTCAAAGAACAAGGAGAATCGCTTGAACCCAGGAGGCGGAGGTTGTGGTGAGCGAAGATCGTGCCATTGCACTCCAGCCTGGGCAACAAGAGCAAAACTCTGTCTCAAAAAAAAAAAAAAGATATAAATCACAATAAATAAATAGGTCAATACAAATGTTGGCCAGGCGTGGTGGCACATGCCCATAGTCGCAGCTACTCTGGAGGCAGAGGCAGGAGGATCACTTGAGCCCATGAATTTGAGGCAGCAGTGAGCTATGATTGTGCCACTGTACTCCAGTCTGGGTGACAGAGTGAGACCCCATCTCTAAATAAATAGGTCAAACCCTTAAAAATATTTAAATTCTTAAAAAAAAAAAAAAA
}

azim58wiki: