Proteome Analyst (PA) is a freely available web server and online toolkit for predicting protein

subcellular localization The cells of eukaryotic organisms are elaborately subdivided into functionally-distinct membrane-bound compartments. Some major constituents of eukaryotic cells are: extracellular space, plasma membrane, cytoplasm, nucleus, mitochondria, Golgi a ...

, or where a protein resides in a cell. In the field of

proteomics Proteomics is the large-scale study of proteins. Proteins are vital macromolecules of all living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replicatio ...

, accurately predicting a protein's

, or where a specific protein is located inside a cell, is an important step in the large scale study of proteins. This computational prediction problem is known as Protein subcellular localization prediction. Over the last decade, more than a dozen web servers and computer programs have been developed to attempt to solve this problem. Proteome Analyst is an example of one of the better performing subcellular prediction tools. Proteome Analyst makes predictions for both prokaryotic eukaryotic proteins using a

text mining Text mining, text data mining (TDM) or text analytics is the process of deriving high-quality information from text. It involves "the discovery by computer of new, previously unknown information, by automatically extracting information from differe ...

approach. Proteome Analyst was originally developed by the Proteome Analyst Research Group at the University of Alberta, and was initially released in March 2004. It was recently updated in January 2014.

Input/Output and Method

Users can submit requests to the Proteome Analyst web server by selecting the organism type and then uploading a text file containing the protein sequence in a FASTA format. Proteome Analyst then uses BLAST to look for similar proteins in the

Uniprot UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived fro ...

database with annotation on

information. Proteome Analyst then uses a machine-learned classifier to analyze the annotation text fields of the most similar proteins identified in Uniprot search to make the final subcellular localization predictions. Users can view and download Proteome Analyst's results or ask Proteome Analyst to explain its predictions.

Technology

Proteome Analyst consists of >30,000 lines of Java code and can be deployed on computer cluster to accelerate its speed and performance using multiple CPUs. The initial release of Proteome Analyst used Naïve Bayes classifier to perform its predictions. The current version of Proteome Analyst uses Support Vector Machine classifiers. Currently Proteome Analyst supports subcellular predictions for five organism types (Eurkayotes including animal, plant,

fungi A fungus (: fungi , , , or ; or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and mold (fungus), molds, as well as the more familiar mushrooms. These organisms are classified as one ...

, and

prokaryotes A prokaryote (; less commonly spelled procaryote) is a single-celled organism whose cell lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Ancient Greek (), meaning 'before', and (), meaning 'nut' ...

including

gram-positive In bacteriology, gram-positive bacteria are bacteria that give a positive result in the Gram stain test, which is traditionally used to quickly classify bacteria into two broad categories according to their type of cell wall. The Gram stain is ...

and

gram-negative Gram-negative bacteria are bacteria that, unlike gram-positive bacteria, do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. Their defining characteristic is that their cell envelope consists ...

bacteria).

References

{{reflist Protein databases

Input/Output and Method

Technology

See also

References