A nonparametric model for quality control of database search results in shotgun proteomics

Background  

Analysis of complex samples with tandem mass spectrometry (MS/MS) has become routine in proteomic research. However, validation of database search results creates a bottleneck in MS/MS data processing. Recently, methods based on a randomized database have become popular for quality control of database search results. However, a consequent problem is the ignorance of how to combine different database search scores to improve the sensitivity of randomized database methods.     

A genomic island present along the bacterial chromosome of the <Emphasis Type="Italic">Parachlamydiaceae</Emphasis> UWE25, an obligate amoebal endosymbiont,encodes a potentially functional F-like conjugative DNA transfer system

Background  

The genome of Protochlamydia amoebophila UWE25, a Parachlamydia-related endosymbiont of free-living amoebae, was recently published, providing the opportunity to search for genomic islands (GIs).     

Calibrating E-values for MS2 database search methods

Background  

The key to mass-spectrometry-based proteomics is peptide identification, which relies on software analysis of tandem mass spectra. Although each search engine has its strength, combining the strengths of various search engines is not yet realizable largely due to the lack of a unified statistical framework that is applicable to any method.     

Analysis by <Emphasis Type="Italic">siRNA_profile</Emphasis> program displays novel thermodynamic characteristics of highly functional siRNA molecules

Objective  

Here we report the improved results of a new siRNA design program and analysis tool called siRNA_profile that reveals an additional criterion for bioinformatic search of highly functional siRNA sequences.     

Mechanisms for stabilisation and the maintenance of solubility in proteins from thermophiles

Background  

The database of protein structures contains representatives from organisms with a range of growth temperatures. Various properties have been studied in a search for the molecular basis of protein adaptation to higher growth temperature. Charged groups have emerged as key distinguishing factors for proteins from thermophiles and mesophiles.     

Hidden Markov model speed heuristic and iterative HMM search procedure

Background  

Profile hidden Markov models (profile-HMMs) are sensitive tools for remote protein homology detection, but the main scoring algorithms, Viterbi or Forward, require considerable time to search large sequence databases.     

Triad pattern algorithm for predicting strong promoter candidates in bacterial genomes

Background  

Bacterial promoters, which increase the efficiency of gene expression, differ from other promoters by several characteristics. This difference, not yet widely exploited in bioinformatics, looks promising for the development of relevant computational tools to search for strong promoters in bacterial genomes.     

Hubs of knowledge: using the functional link structure in Biozon to mine for biologically significant entities

Background  

Existing biological databases support a variety of queries such as keyword or definition search. However, they do not provide any measure of relevance for the instances reported, and result sets are usually sorted arbitrarily.     

Identification of biomarkers for genotyping <Emphasis Type="Italic">Aspergilli</Emphasis> using non-linear methods for clustering and classification

Background  

In the present investigation, we have used an exhaustive metabolite profiling approach to search for biomarkers in recombinantAspergillus nidulans(mutants that produce the 6- methyl salicylic acid polyketide molecule) for application in metabolic engineering.     

A Dynamic Noise Level Algorithm for Spectral Screening of Peptide MS/MS Spectra

Background  

High-throughput shotgun proteomics data contain a significant number of spectra from non-peptide ions or spectra of too poor quality to obtain highly confident peptide identifications. These spectra cannot be identified with any positive peptide matches in some database search programs or are identified with false positives in others. Removing these spectra can improve the database search results and lower computational expense.     

PseudoGeneQuest – Service for identification of different pseudogene types in the human genome

Background  

Pseudogenes, nonfunctional copies of genes, evolve fast due the lack of evolutionary pressures and thus appear in several different forms. PseudoGeneQuest is an online tool to search the human genome for a given query sequence and to identify different types of pseudogenes as well as novel genes and gene fragments.     

Large scale hierarchical clustering of protein sequences

Background  

Searching a biological sequence database with a query sequence looking for homologues has become a routine operation in computational biology. In spite of the high degree of sophistication of currently available search routines it is still virtually impossible to identify quickly and clearly a group of sequences that a given query sequence belongs to.     

Similarity searches in genome-wide numerical data sets

   

We present psi-square, a program for searching the space of gene vectors. The program starts with a gene vector, i.e., the set of measurements associated with a gene, and finds similar vectors, derives a probabilistic model of these vectors, then repeats search using this model as a query, and continues to update the model and search again, until convergence. When applied to three different pathway-discovery problems, psi-square was generally more sensitive and sometimes more specific than the ad hoc methods developed for solving each of these problems before.     

In vivo killing of Staphylococcus aureus using a light-activated antimicrobial agent

Background  

The widespread problem of antibiotic resistance in pathogens such as Staphylococcus aureus has prompted the search for new antimicrobial approaches. In this study we report for the first time the use of a light-activated antimicrobial agent, methylene blue, to kill an epidemic methicillin-resistant Staphylococcus aureus (EMRSA-16) strain in two mouse wound models.     

A stitch in time: Efficient computation of genomic DNA melting bubbles

Background  

It is of biological interest to make genome-wide predictions of the locations of DNA melting bubbles using statistical mechanics models. Computationally, this poses the challenge that a generic search through all combinations of bubble starts and ends is quadratic.     

Discovery of serum biomarkers of alcoholic fatty liver in a rodent model: C-reactive protein

Background  

Excessive consumption of alcohol contributes to alcoholic liver disease. Fatty liver is the early stage of alcohol-related liver disease. The aim of this study was to search for specific serological biomarkers of alcoholic fatty liver (AFL) compared to healthy controls, non-alcoholic fatty liver (NAFL) and liver fibrosis in a rodent model.