SMC hit investigation 12-15-12

2015-01-13

azim58 - SMC hit investigation 12-15-12

Dr. Johnston is interested in whether or not the SMC hits from the PMRE
and HEE epitopes match up with the original frameshift sequence.

Here is the sequence of the human SMC1fs sequence

Human smc-1: TAIIGPNGSGCCGIYCHEEPQREDSSI

Diagram of SMC1fs constructs can be found here
C:\kurt\storage\CIM Research Folder\DR\2012\7-21-12

Note that the rabbits in the paper shen and I are working on were
immunized with KLH conjugated to the human SMC1fs sequence part
containing only the 17 aa acids of frameshift sequence (the part in red
above).

Here are the BLAST results that were previously done.

Here's the HEEX blast

"S:\Research\Cancer_Eradication\Users\kwhittem\DR\2012\9-27-12\test_blast\t
est_for_hee.txt"

Here's the PMRE blast

"S:\Research\Cancer_Eradication\Users\kwhittem\DR\2012\9-27-12\test_blast\t
est_for_pmre.txt"

Now I would like to make two tables comparing the HEE SMC hit sequences
with the original human frameshift sequence.
Tables found here
C:\kurt\storage\CIM Research Folder\DR\2012\12-16-12\SMC hit analysis

None of the SMC hits match the original frameshift sequence. However,
some of the hits do have sequence that is somewhat similar to the human
SMC1fs sequence

===========================================================================
12-17-12
HEEPQRE Human BLAST results
"C:\kurt\storage\CIM Research Folder\DR\2012\12-17-12\HEEPQRE human BLAST
results.txt"

pmre human website blast results
"C:\kurt\storage\CIM Research Folder\DR\2012\12-17-12\pmre human website
blast results.txt"

===========================================================================
12-24-12

Searched human sequences using the following command.
blastp -db S:\Research\BLAST_nr_database\nr -gilist
S:\Research\BLAST_gi_lists\human_gi_list.gi.txt -query
"C:\kurt\storage\CIM Research Folder\DR\2012\12-24-12\SMC hit
analysis\heex" -word_size 2 -seg no -evalue 200000000000000
-comp_based_stats no -matrix pam30 -threshold 4 -num_descriptions 20000
-num_alignments 0 -out "C:\kurt\storage\CIM Research
Folder\DR\2012\12-24-12\SMC hit analysis\hee_blast_output.txt"

Data found here
C:\kurt\storage\CIM Research Folder\DR\2012\12-24-12\SMC hit analysis

I also did some searches with heepqre, ccgiy, and hsmc1fs.
Example blast command
blastp -db S:\Research\BLAST_nr_database\nr -gilist
S:\Research\BLAST_gi_lists\human_gi_list.gi.txt -query
"S:\Research\Cancer_Eradication\Users\kwhittem\kwhittem\Raw Data Often
Originally on Research Drive\2012\12-24-12\smc_analysis\heepqre"
-word_size 2 -seg no -evalue 200000000000000 -comp_based_stats no -matrix
pam30 -threshold 4 -num_descriptions 20000 -num_alignments 0 -out
"S:\Research\Cancer_Eradication\Users\kwhittem\kwhittem\Raw Data Often
Originally on Research
Drive\2012\12-24-12\smc_analysis\heepqre_blast_output.txt"

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