UPS 2.0: unique probe selector for probe design and oligonucleotide microarrays at the pangenomic/ genomic level

<p>Abstract</p> <p>Background</p> <p>Nucleic acid hybridization is an extensively adopted principle in biomedical research, in which the performance of any hybridization-based method depends on the specificity of probes to their targets. To determine the optimal probe(s) for detecting target(s) from a sample cocktail, we developed a novel algorithm, which has been implemented into a web platform for probe designing. This probe design workflow is now upgraded to satisfy experiments that require a probe designing tool to take the increasing volume of sequence datasets.</p> <p>Results</p> <p>Algorithms and probe parameters applied in UPS 2.0 include GC content, the secondary structure, melting temperature (Tm), the stability of the probe-target duplex estimated by the thermodynamic model, sequence complexity, similarity of probes to non-target sequences, and other empirical parameters used in the laboratory. Several probe background options,<b><it>Unique probe within a group</it></b><it>,</it><b><it>Unique probe in a specific Unigene set</it></b><it>,</it><b><it>Unique probe based onthe pangenomic level</it></b><it>,</it> and <b><it>Unique Probe in the user-defined genome/transcriptome</it></b><it>,</it> are available to meet the scenarios that the experiments will be conducted. Parameters, such as salt concentration and the lower-bound Tm of probes, are available for users to optimize their probe design query. Output files are available for download on the result page. Probes designed by the UPS algorithm are suitable for generating microarrays, and the performance of UPS-designed probes has been validated by experiments.</p> <p>Conclusions</p> <p>The UPS 2.0 evaluates probe-to-target hybridization under a user-defined condition to ensure high-performance hybridization with minimal chance of non-specific binding at the pangenomic and genomic levels. The UPS algorithm mimics the target/non-target mixture in an experiment and is very useful in developing diagnostic kits and microarrays. The UPS 2.0 website has had more than 1,300 visits and 360,000 sequences performed the probe designing task in the last 30 months. It is freely accessible at <url>http://array.iis.sinica.edu.tw/ups/.</url></p> <p>Screen cast: <url>http://array.iis.sinica.edu.tw/ups/demo/demo.htm</url></p

PALM: A Paralleled and Integrated Framework for Phylogenetic Inference with Automatic Likelihood Model Selectors

BACKGROUND: Selecting an appropriate substitution model and deriving a tree topology for a given sequence set are essential in phylogenetic analysis. However, such time consuming, computationally intensive tasks rely on knowledge of substitution model theories and related expertise to run through all possible combinations of several separate programs. To ensure a thorough and efficient analysis and avert tedious manipulations of various programs, this work presents an intuitive framework, the phylogenetic reconstruction with automatic likelihood model selectors (PALM), with convincing, updated algorithms and a best-fit model selection mechanism for seamless phylogenetic analysis. METHODOLOGY: As an integrated framework of ClustalW, PhyML, MODELTEST, ProtTest, and several in-house programs, PALM evaluates the fitness of 56 substitution models for nucleotide sequences and 112 substitution models for protein sequences with scores in various criteria. The input for PALM can be either sequences in FASTA format or a sequence alignment file in PHYLIP format. To accelerate the computing of maximum likelihood and bootstrapping, this work integrates MPICH2/PhyML, PalmMonitor and Palm job controller across several machines with multiple processors and adopts the task parallelism approach. Moreover, an intuitive and interactive web component, PalmTree, is developed for displaying and operating the output tree with options of tree rooting, branches swapping, viewing the branch length values, and viewing bootstrapping score, as well as removing nodes to restart analysis iteratively. SIGNIFICANCE: The workflow of PALM is straightforward and coherent. Via a succinct, user-friendly interface, researchers unfamiliar with phylogenetic analysis can easily use this server to submit sequences, retrieve the output, and re-submit a job based on a previous result if some sequences are to be deleted or added for phylogenetic reconstruction. PALM results in an inference of phylogenetic relationship not only by vanquishing the computation difficulty of ML methods but also providing statistic methods for model selection and bootstrapping. The proposed approach can reduce calculation time, which is particularly relevant when querying a large data set. PALM can be accessed online at http://palm.iis.sinica.edu.tw

Fly-DPI: database of protein interactomes for D. melanogaster in the approach of systems biology

BACKGROUND: Proteins control and mediate many biological activities of cells by interacting with other protein partners. This work presents a statistical model to predict protein interaction networks of Drosophila melanogaster based on insight into domain interactions. RESULTS: Three high-throughput yeast two-hybrid experiments and the collection in FlyBase were used as our starting datasets. The co-occurrences of domains in these interactive events are converted into a probability score of domain-domain interaction. These scores are used to infer putative interaction among all available open reading frames (ORFs) of fruit fly. Additionally, the likelihood function is used to estimate all potential protein-protein interactions. All parameters are successfully iterated and MLE is obtained for each pair of domains. Additionally, the maximized likelihood reaches its converged criteria and maintains the probability stable. The hybrid model achieves a high specificity with a loss of sensitivity, suggesting that the model may possess major features of protein-protein interactions. Several putative interactions predicted by the proposed hybrid model are supported by literatures, while experimental data with a low probability score indicate an uncertain reliability and require further proof of interaction. Fly-DPI is the online database used to present this work. It is an integrated proteomics tool with comprehensive protein annotation information from major databases as well as an effective means of predicting protein-protein interactions. As a novel search strategy, the ping-pong search is a naïve path map between two chosen proteins based on pre-computed shortest paths. Adopting effective filtering strategies will facilitate researchers in depicting the bird's eye view of the network of interest. Fly-DPI can be accessed at . CONCLUSION: This work provides two reference systems, statistical and biological, to evaluate the reliability of protein interaction. First, the hybrid model statistically estimates both experimental and predicted protein interaction relationships. Second, the biological information for filtering and annotation itself is a strong indicator for the reliability of protein-protein interaction. The space-temporal or stage-specific expression patterns of genes are also critical for identifying proteins involved in a particular situation

Effect of shaking process on correlations between catechins and volatiles in oolong tea

AbstractShaking the tea leaves is the key manipulation to making oolong tea. It contributes to the formation of flavor and fragrance in oolong tea. The dynamic variations of catechins and volatile organic compounds (VOCs) during the shaking process were investigated. The results showed that the contents of epicatechin, epigallocatechin, epicatechin gallate (ECG), and epigallocatechin gallate (EGCG) first decreased after the shaking and then increased to the initial value before the next shaking. Geraniol, linalool and its oxides, and phenylethyl alcohol showed similar variations. The contents of trans-β-ocimene, 1H-indole, and 3-hexenyl hexanoate increased after the second or third shaking (the late fermentation stage). However, the contents of aldehydes showed an opposite trend to other VOCs. The abundance of phenylethyl alcohol was positively related to the content of ECG and EGCG ​during fermentation, whereas the abundance of cis-3-hexenal was negatively related to the content of ECG. The correlations between catechin and VOCs indicated that shaking affected the chemical transformation of the compounds in oolong tea

Functional Proteomics in Silico: Putative Protein Interaction Analysis

During the past few years, protein interaction networks of some viral, prokaryotic and eukaryotic species have been established gradually. The proteome of those organisms were used as alignment templates to identify novel genes in different species. Many studies also support that the functional related proteins of different species were regulated in similar mechanism, suggested the evolutionaril