pTARGET: a web server for predicting protein subcellular localization

The pTARGET web server enables prediction of nine distinct protein subcellular localizations in eukaryotic non-plant species. Predictions are made using a new algorithm [C. Guda and S. Subramaniam (2005) pTARGET [corrected] a new method for predicting protein subcellular localization in eukaryotes. Bioinformatics, 21, 3963–3969], which is primarily based on the occurrence patterns of location-specific protein functional domains in different subcellular locations. We have implemented a relational database, PreCalcDB, to store pre-computed prediction results for all eukaryotic non-plant protein sequences in the public domain that includes about 770 000 entries. Queries can be made by entering protein sequences or by uploading a file containing up to 5000 protein sequences in FASTA format. Prediction results for queries with matching entries in the PreCalcDB will be retrieved instantly; while for the missing ones new predictions will be computed and sent by email. Pre-computed predictions can also be downloaded for complete proteomes of Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila, Mus musculus and Homo sapiens. The server, its documentation and the data are accessible from

The Ignition And The Mass

I may not remember muchAbout this day.I may not recall specifics,What exactly happened when~ excerpt from poe

Alone Tonight

Somehow it’s just not rightThat I should sit alone tonight.The rain comes downWhile melodic soundsCreep inside to meet me. ~excerpt from poe

Odorants for surveillance and control of the Asian Citrus Psyllid (Diaphorina citri).

BackgroundThe Asian Citrus Psyllid (ACP), Diaphorina citri, can transmit the bacterium Candidatus Liberibacter while feeding on citrus flush shoots. This bacterium causes Huanglongbing (HLB), a major disease of citrus cultivation worldwide necessitating the development of new tools for ACP surveillance and control. The olfactory system of ACP is sensitive to variety of odorants released by citrus plants and offers an opportunity to develop new attractants and repellents.ResultsIn this study, we performed single-unit electrophysiology to identify odorants that are strong activators, inhibitors, and prolonged activators of ACP odorant receptor neurons (ORNs). We identified a suite of odorants that activated the ORNs with high specificity and sensitivity, which may be useful in eliciting behavior such as attraction. In separate experiments, we also identified odorants that evoked prolonged ORN responses and antagonistic odorants able to suppress neuronal responses to activators, both of which can be useful in lowering attraction to hosts. In field trials, we tested the electrophysiologically identified activating odorants and identified a 3-odor blend that enhances trap catches by ∼230%.ConclusionThese findings provide a set of odorants that can be used to develop affordable and safe odor-based surveillance and masking strategies for this dangerous pest insect

Attached To Me

If I flew away from youAnd left youWould I stayIn your thoughtsAnd in your dreams?Would I help you to be brave? ~excerpt from poe

A Top-Down Approach to Infer and Compare Domain-Domain Interactions across Eight Model Organisms

Knowledge of specific domain-domain interactions (DDIs) is essential to understand the functional significance of protein interaction networks. Despite the availability of an enormous amount of data on protein-protein interactions (PPIs), very little is known about specific DDIs occurring in them. Here, we present a top-down approach to accurately infer functionally relevant DDIs from PPI data. We created a comprehensive, non-redundant dataset of 209,165 experimentally-derived PPIs by combining datasets from five major interaction databases. We introduced an integrated scoring system that uses a novel combination of a set of five orthogonal scoring features covering the probabilistic, evolutionary, evidence-based, spatial and functional properties of interacting domains, which can map the interacting propensity of two domains in many dimensions. This method outperforms similar existing methods both in the accuracy of prediction and in the coverage of domain interaction space. We predicted a set of 52,492 high-confidence DDIs to carry out cross-species comparison of DDI conservation in eight model species including human, mouse, Drosophila, C. elegans, yeast, Plasmodium, E. coli and Arabidopsis. Our results show that only 23% of these DDIs are conserved in at least two species and only 3.8% in at least 4 species, indicating a rather low conservation across species. Pair-wise analysis of DDI conservation revealed a ‘sliding conservation’ pattern between the evolutionarily neighboring species. Our methodology and the high-confidence DDI predictions generated in this study can help to better understand the functional significance of PPIs at the modular level, thus can significantly impact further experimental investigations in systems biology research

Evaluation of Email Spam Detection Techniques

Email has become a vital form of communication among individuals and organizations in today’s world. However, simultaneously it became a threat to many users in the form of spam emails which are also referred as junk/unsolicited emails. Most of the spam emails received by the users are in the form of commercial advertising, which usually carry computer viruses without any notifications. Today, 95% of the email messages across the world are believed to be spam, therefore it is essential to develop spam detection techniques. There are different techniques to detect and filter the spam emails, but off recently all the developed techniques are being implemented successfully to minimize the threats. This paper describes how the current spam email detection approaches are determining and evaluating the problems. There are different types of techniques developed based on Reputation, Origin, Words, Multimedia, Textual, Community, Rules, Hybrid, Machine learning, Fingerprint, Social networks, Protocols, Traffic analysis, OCR techniques, Low-level features, and many other techniques. All these filtering techniques are developed to detect and evaluate spam emails. Along with classification of the email messages into spam or ham, this paper also demonstrates the effectiveness and accuracy of the spam detection techniques

ISO STANDARDS FOR AIR SYSTEMS

Air system is a system of mechanical refrigeration in which cold air is compressed, cooled, and permitted to expand and thus acts as the refrigerating agent. International Standards bring technological, economic and social benefits. This article provides an introduction to the ISO 8573 and ISO 12500 series of International Standards which cover compressed air purity and test methods, as well as the purification equipment essential to achieve the standards. The amount of water present in a compressed air system is staggering. Combination of a small 2.8 m3/min (100 scfm) compressor and refrigeration dryer, operating for 4000 hours in typical Northern European climatic conditions can produce approximately 10,000 litres or 2,200 gallons of liquid condensate per year. If the compressor is oil lubricated with a typical 2 mg/m3 (2ppm) oil carryover, then though the resulting condensate would visually resemble oil, oil would in fact account for less than 0.1% of the overall volume and it is this resemblance to oil to which a false association is made. Testing standards are being revised to give the users an unblemished picture of how components will perform. These standards are being written to help users manage their total energy consumption. In order to help users evaluate their compressed air systems, additional standards are about to release and these newer standards can have significant impact on plant energy consumption if properly applied