למי שרוצה או שאל - הנה המאמר
One Article, hot off the digital press.
"NeuroPID: A Predictor for Identifying Neuropeptide Precursors from Metazoan Proteomes"
If anyone wants to read it, and lacks academic access, send me a PM or email, and i'll provide you with an open-access link + a copy of the article.
NeuroPID: A Predictor for Identifying Neuropeptide Precursors from Metazoan Proteomes
Dan Ofer and Michal Linial,*
1Department of Biological Chemistry, Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Givat Ram, 91904, Israel
↵*
Motivation: The evolution of multicellular organisms is associated with increasing variability of molecules governing behavioral and physiological states. This is often achieved by Neuropeptides (NPs) that are produced in neurons from a longer protein, named neuropeptide precursor (NPP). The maturation of NPs occurs through a sequence of proteolytic cleavages. The difficulty in identifying NPPs is a consequence of their diversity and the lack of applicable sequence similarity among the short, functionally related NPs.
Results: Herein, we describe NeuroPID, a machine-learning scheme that predicts Metazoan NPPs. NeuroPID was trained on hundreds of identified NPPs from the UniProtKB database. Some 600 features were extracted from the primary sequences and processed using support vector machines (SVM) and ensemble decision tree classifiers. These features combined biophysical, chemical and informational-statistical properties of NPs and NPPs. Other features were guided by the defining characteristics of the dibasic cleavage sites motif. NeuroPID reached 89-94% accuracy and 90-93% precision in cross-validation blind tests against known NPPs (with an emphasis on Chordata and Arthropoda). NeuroPID also identified NPP-like proteins from extensively studied model organisms as well as from poorly annotated proteomes. We then focused on the most significant sets of features that contribute to the success of the classifiers. We propose that NPPs are attractive targets for investigating and modulating behavior, metabolism and homeostasis, and that a rich repertoire of NPs remains to be identified.
Photography Genius is always allowed some leeway, once the hammer has been pried from its hands and the blood has been cleaned up.
To improve is to change; to be perfect is to change often.
Never apologise for being a geek, because they won't apologise to you for being an arsehole. John Barrowman - 22 June 2014 Perth Supernova.
Countries I have been to - 14.
Australia, Canada, China, Colombia, Denmark, Ecuador, Finland, Germany, Malaysia, Netherlands, Norway, Singapore, Sweden, USA.
Always on the lookout for more nice places to visit.
Yeah, I've always taken the subtext of the Birther movement to be, "The rules don't count here! This is different! HE'S BLACK! BLACK, I SAY! ARE YOU ALL BLIND!?
- Raw Shark
Destiny and fate are for those too weak to forge their own futures. Where we are 'supposed' to be is irrelevent.
Congratulations. Is there a tl;dr version for dummies?
A minute's thought suggests that the very idea of this is stupid. A more detailed examination raises the possibility that it might be an answer to the question "how could the Germans win the war after the US gets involved?" - Captain Seafort, in a thread proposing a 1942 'D-Day' in Quiberon Bay
LaCroix wrote:Congratulations. Is there a tl;dr version for dummies?
In brief : I use supervised binary machine learning classification methods (support vector machines and random forests), in order to identify on the basis of primary (amino acid) sequence functional features alone (I.e, not on the basis of sequence similarity, BLAST or they like) - neuropeptide precursor proteins.
It's simpler than it sounds. Shall I explain machine learning, proteins, or neuropeptides ?
Photography Genius is always allowed some leeway, once the hammer has been pried from its hands and the blood has been cleaned up.
To improve is to change; to be perfect is to change often.
So you were doing sciency stuff to stuff that would become neurotransmitters. Working on your own Khan?
A minute's thought suggests that the very idea of this is stupid. A more detailed examination raises the possibility that it might be an answer to the question "how could the Germans win the war after the US gets involved?" - Captain Seafort, in a thread proposing a 1942 'D-Day' in Quiberon Bay
LaCroix wrote:So you were doing sciency stuff to stuff that would become neurotransmitters. Working on your own Khan?
Neuropeptide are closer to neurohormones than nt actually, and are much more complicated and (consequently) unexplored. This is a predictive measure only, .
Khan Noonien Singh would gmo genetics. I'm more in the vein of "understand!" (Ted Chiang)
Photography Genius is always allowed some leeway, once the hammer has been pried from its hands and the blood has been cleaned up.
To improve is to change; to be perfect is to change often.
