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.