LIPPRED:a web server for accurate prediction of lipoprotein signal sequences and cleavage sites

Bacterial lipoproteins have many important functions and represent a class of possible vaccine candidates. The prediction of lipoproteins from sequence is thus an important task for computational vaccinology. Naïve-Bayesian networks were trained to identify SpaseII cleavage sites and their preceding signal sequences using a set of 199 distinct lipoprotein sequences. A comprehensive range of sequence models was used to identify the best model for lipoprotein signal sequences. The best performing sequence model was found to be 10-residues in length, including the conserved cysteine lipid attachment site and the nine residues prior to it. The sensitivity of prediction for LipPred was 0.979, while the specificity was 0.742. Here, we describe LipPred, a web server for lipoprotein prediction; available at the URL: http://www.jenner.ac.uk/LipPred/. LipPred is the most accurate method available for the detection of SpaseIIcleaved lipoprotein signal sequences and the prediction of their cleavage sites.

Site-restricted web searches for data collection in regional dialectology

This article presents a new method for data collection in regional dialectology based on site-restricted web searches. The method measures the usage and determines the distribution of lexical variants across a region of interest using common web search engines, such as Google or Bing. The method involves estimating the proportions of the variants of a lexical alternation variable over a series of cities by counting the number of webpages that contain the variants on newspaper websites originating from these cities through site-restricted web searches. The method is evaluated by mapping the 26 variants of 10 lexical variables with known distributions in American English. In almost all cases, the maps based on site-restricted web searches align closely with traditional dialect maps based on data gathered through questionnaires, demonstrating the accuracy of this method for the observation of regional linguistic variation. However, unlike collecting dialect data using traditional methods, which is a relatively slow process, the use of site-restricted web searches allows for dialect data to be collected from across a region as large as the United States in a matter of days.