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

2015-01-13

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

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