Work 121111 0942

2015-01-13

azim58 - Work 121111 0942

I want to call an example glam2 command, and I need an example FASTA file
to do this.

183seq.fa
"W:\azim58\wuala\CIM Research Folder\kwhittem\Records in CIM
Folder\Categorical Records\Motif Peptide Analysis\183seq.fa"

cd C:\cygwin\home\Owner\meme\meme_4.6.1\src
glam2 p "W:\azim58\wuala\CIM Research Folder\kwhittem\Records in CIM
Folder\Categorical Records\Motif Peptide Analysis\183seq.fa"

I would like to try comparing just two single peptides to see if I can
use glam2 to give me a score related to the similarity of two peptides.

My two_peptides.fa file will have these two peptides:

>183
CCGIYCHEEPQREDSSI
>134
RVGEMPMREYDISGGSG

The PQRE and PMRE peptides should be quite similar.

Script:

cd C:\cygwin\home\Owner\meme\meme_4.6.1\src
glam2 p "W:\azim58\wuala\CIM Research Folder\kwhittem\Records in CIM
Folder\Categorical Records\Motif Peptide Analysis\two_peptides.fa"

The score I obtained was: 7.12031

What kind of score do I obtain for two non-similar peptides? (not sure
how to pick a non-similar peptide. . .)

Script:
cd C:\cygwin\home\Owner\meme\meme_4.6.1\src
glam2 p "W:\azim58\wuala\CIM Research Folder\kwhittem\Records in CIM
Folder\Categorical Records\Motif Peptide
Analysis\two_non-similar_peptides.fa"

The score I obtained was: 4.65858
Okay, this seems to be working. I obtained a lower score as expected and
desired. I can probably go ahead and try to implement this in some Java
code now.

Here's the score information I obtained for that:

===========================================================================
Score: 4.65858 Columns: 5 Sequences: 2

*
183 4 IYCHE 8 + 4.66
125 2 FFFHK 6 + 4.67

===========================================================================

I wrote some code, but it looks like I'll have to resolve this error:

===========================================================================
There was an error: Cannot run program "glam2" (in directory
"C:\cygwin\home\Owner\meme\meme_4.6.1\src"): CreateProcess error=2, The
system cannot find the file specified

===========================================================================

I think I might remember something like this. I think the code is not
recognizing that it should call this glam2 directory with cygwin because
it is not using the correct system path variables or something. I'll have
to look into this more later.

azim58wiki: