GLAM2

2015-01-13

azim58 - GLAM2

GLAM2: this program will try to find the best motif when given several
sequences, and the program will assign a score to the motif.

The program accepts a fasta file as input.
Example command:
glam2 p 183seq.fa -o test

The program outputs a meme file, as well as many other files (including an html file) in a folder
For more information on the meme file format see:
http://pgfe.umassmed.edu/meme/doc/meme-format.html

For an example meme file see:
"C:\Users\kurtw_000\Documents\kurt\storage\lgdata_DR\2014\01-16-2014d1422\selected young aged gprs\decipher for 100 peptides by age 3 criteria\analysis of josh\glam2\motifs from pasting each epitope 3 times no zeros.meme"

What is a good glam2 score?
Higher scores in glam2 are better.  However, the scores seem relative to the number of sequences input and other factors.  Therefore, it may be hard to compare scores from one input with scores from another input.  However, with inputs that have approximately the same number of input sequences then higher scores are better.

Some Java code for using glam2 can be found here
-C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2012\10-2-12\code\mpa src 10-3-12
--associated page here: [Motif Peptide Analysis]

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