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Gene set enrichment analyses revealed differences in gene expression patterns between males and females.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Men and women differ not only in their physical attributes and reproductive functions but also in many other characteristics, including the risks for some diseases as well as response to certain therapeutic treatments. Though genetically-identical for autosomal chromosomes, males and females could have gender-specific transcriptional or translational regulation, leading to differential mRNAs or protein products for some genes. To illustrate the gender-specific differences in mRNA-level expression, we compared gene expression patterns between males and females using a whole-genome microarray dataset on the unrelated Hap...
Source: In Silico Biol - October 4, 2009 Category: Biology Authors: Zhang W, Huang RS, Duan S, Dolan ME Tags: In Silico Biol Source Type: journals

Classification of information fusion methods in systems biology.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Biological systems are extremely complex and often involve thousands of interacting components. Despite all efforts, many complex biological systems are still poorly understood. However, over the past few years high-throughput technologies have generated large amounts of biological data, now requiring advanced bioinformatic algorithms for interpretation into valuable biological information. Due to these high-throughput technologies, the study of biological systems has evolved from focusing on single components (e.g. genes) to encompassing large sets of components (e.g. all genes in an entire genome), with the aim to el...
Source: In Silico Biol - October 4, 2009 Category: Biology Authors: Synnergren J, Olsson B, Gamalielsson J Tags: In Silico Biol Source Type: journals

Numerical characterization of protein sequences and application to voltage-gated sodium channel alpha subunit phylogeny.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We propose a new method to compare sequences of protein families by generating numerical characterizations through a 20D representation. Using a walk along the axes representing the amino acids we generate a vector for each sequence whose components can be used to derive distance matrices between sequences and whose magnitudes can be used to compare the similarities/dissimilarities between the different sequences. The distance matrices enable creation of phylogenetic trees without need for multiple alignments or any other model dependencies. In this paper we test this technique with human globin gene sequences and then...
Source: In Silico Biol - October 4, 2009 Category: Biology Authors: Nandy A, Ghoshb A, Nandy P Tags: In Silico Biol Source Type: journals

Remote homology detection using a kernel method that combines sequence and secondary-structure similarity scores.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Distant evolutionary relationships between proteins with low sequence similarity are difficult to recognise by computational methods. Consequently, many sequences obtained from large-scale sequencing projects cannot be assigned to any known proteins or families despite being evolutionarily related. To boost sensitivity, various sequence-based methods have been modified to make use of the better conserved secondary structure. Most of these methods are instance-based or generative. Here, we introduce a kernel-based remote homology detection method that allows for a combination of sequence and secondary-structure similari...
Source: In Silico Biol - October 4, 2009 Category: Biology Authors: Wieser D, Niranjan M Tags: In Silico Biol Source Type: journals

Determinants for psychrophilic and thermophilic features of metallopeptidases of the M4 family.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Naturally occurring peptidases from organisms living under extreme conditions are adapted to function in environmental extremes, including temperature, salinity, pH, or pressure. These organisms represent unique sources for new bio-molecules that have both industrial and medicinal application. Adaptive strategies for functioning under extreme conditions are reflected at the enzyme sequence and structural level. Understanding the determinants responsible for unique functional features can be used to enhance the functional features of known proteins. In the present study, the amino acid sequences of 81 peptidases of the ...
Source: In Silico Biol - October 4, 2009 Category: Biology Authors: Khan MT, Sylte I Tags: In Silico Biol Source Type: journals

Empowering spot detection in 2DE images by wavelet denoising.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Typical high-abundant proteins, including albumin, IgG, IgA and others, are the target of depletion methods usually applied to two-dimensional electrophoresis (2DE) of human biological fluids like serum and plasma. Detection of low-abundant proteins is of interest with regard to biomarkers for disease when being studied by 2DE or liquid chromatography-mass spectrometry (LC/MS). After depletion of very abundant proteins, serum samples consist of an enriched pool of low-abundant proteins that can be further studied without significant interferences, thus allowing for a full identification of the low abundant proteins, wh...
Source: In Silico Biol - October 4, 2009 Category: Biology Authors: Soggiu A, Marullo O, Roncada P, Capobianco E Tags: In Silico Biol Source Type: journals

Prediction of polyadenylation signals in human DNA sequences using nucleotide frequencies.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, Support Vector Machine (SVM) models have been developed for predicting poly(A) signals in a DNA sequence using 100 nucleotides, each upstream and downstream of this signal. Here, we introduced a novel split nucleotide frequency technique, and the models thus developed achieved maximum Matthews correlation coefficients (MCC) of 0.58, 0.69, 0.70 and 0.69 using mononucleotide, dinucleotide, trinucleotide, and tetranucleotide frequencies, respectively. Finally, a hybrid model developed using a combination of dinucleotide, 2nd order dinucleotide and tetranucleotide frequencies, achieved a maximum MCC of 0.72. Mor...
Source: In Silico Biol - October 4, 2009 Category: Biology Authors: Ahmed F, Kumar M, Raghava GP Tags: In Silico Biol Source Type: journals

Temperature influences synonymous codon and amino acid usage biases in the phages infecting extremely thermophilic prokaryotes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
To see the effect of temperature on the codon and amino acid usage in phages, codon and amino acid usage of 13 phages of extremely thermophilic prokaryotes were compared with that of 14 phages of mesophilic prokaryotes. Correspondence analysis on RSCU values of two groups of phage genomes clearly shows that phages are separated along the second major axis according to their growth temperature, whereas, they are separated along the first major axis according to their GC content. Correspondence analysis on RAAU values of two groups of phages clearly shows that protein encoding genes of the phages along the second major a...
Source: In Silico Biol - June 28, 2009 Category: Biology Authors: Sau K, Deb A Tags: In Silico Biol Source Type: journals

The SiteSeeker motif discovery tool.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this paper we describe some utilizing conditions of a recently published tool that offers two basic functions for the classical problem of discovering motifs in a set of promoter sequences. For the first it is assumed that not necessarily all of the sequences possess a common motif of given length l. In this case, CHECKPROMOTER allows an exact identification of maximal subsets of related promoters. The purpose of this program is to recognize putatively co-regulated genes. The second, CHECKMOTIF, solves the problem of checking if the given promoters have a common motif. It uses a fast approximation algorithm for whic...
Source: In Silico Biol - June 28, 2009 Category: Biology Authors: Ecker K, Lichtenberg J, Welch L Tags: In Silico Biol Source Type: journals

A Naive Bayes classifier for protein function prediction.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A Naive Bayes classifier tool is presented for annotating proteins on the basis of amino acid motifs, cellular localization and protein-protein interactions. Annotations take the form of posterior probabilities within the Molecular Function hierarchy of the Gene Ontology (GO). Experiments with the data available for yeast, Saccharomyces cerevisiae, show that our prediction method can yield a relatively high level of accuracy. Several apparent challenges and possibilities for future developments are also discussed. A common approach to functional characterization is to use sequence similarities at varying levels, by uti...
Source: In Silico Biol - June 28, 2009 Category: Biology Authors: Kohonen J, Talikota S, Corander J, Auvinen P, Arjas E Tags: In Silico Biol Source Type: journals

SubCellProt: predicting protein subcellular localization using machine learning approaches.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
High-throughput genome sequencing projects continue to churn out enormous amounts of raw sequence data. However, most of this raw sequence data is unannotated and, hence, not very useful. Among the various approaches to decipher the function of a protein, one is to determine its localization. Experimental approaches for proteome annotation including determination of a protein's subcellular localizations are very costly and labor intensive. Besides the available experimental methods, in silico methods present alternative approaches to accomplish this task. Here, we present two machine learning approaches for prediction ...
Source: In Silico Biol - June 28, 2009 Category: Biology Authors: Garg P, Sharma V, Chaudhari P, Roy N Tags: In Silico Biol Source Type: journals

In silico analysis of evolutionary patterns in restriction endonucleases.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Restriction endonucleases represent one of the best studied examples of DNA binding proteins. Type II restriction endonucleases recognize short sequences of foreign DNA and cleave the target on both strands with remarkable sequence specificity. Type II restriction endonucleases are part of restriction modification systems. Restriction modification systems occur ubiquitously among bacteria and archaea. Restriction endonucleases are indispensable tools in molecular biology and biotechnology. They are important model system for specific protein-nucleic acid interactions and also serve as good example for investigating str...
Source: In Silico Biol - June 28, 2009 Category: Biology Authors: Singh TR, Pardasani KR Tags: In Silico Biol Source Type: journals

Analysis of n-gram based promoter recognition methods and application to whole genome promoter prediction.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Promoter prediction is an important and complex problem. Pattern recognition algorithms typically require features that could capture this complexity. A special bias towards certain combinations of base pairs in the promoter sequences may be possible. In order to determine these biases n-grams are usually extracted and analyzed. An n-gram is a selection of n contiguous characters from a given character stream, DNA sequence segments in this case. Here a systematic study is made to discover the efficacy of n-grams for n = 2, 3, 4, 5 in promoter prediction. A study of n-grams as features for a neural network classifier fo...
Source: In Silico Biol - June 28, 2009 Category: Biology Authors: Rani TS, Bapi RS Tags: In Silico Biol Source Type: journals

Extracting signature motifs from promoter sets of differentially expressed genes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study therefore illustrates the power of using relevant biological information, in the form of a set of differentially expressed genes that is a classical outcome in most of transcriptomics studies. This allows to severely reduce the search space and to design an adapted statistical indicator. Taken together, this allows the biologist to concentrate on a small number of putatively interesting TFs. PMID: 19537163 [PubMed - in process] (Source: In Silico Biol)
Source: In Silico Biol - June 28, 2009 Category: Biology Authors: Mitasiŭnaite I, Rigotti C, Schicklin S, Meyniel L, Boulicaut JF, Gandrillon O Tags: In Silico Biol Source Type: journals

Molecular and structural basis of drift in the functions of closely-related homologous enzyme domains: implications for function annotation based on homology searches and structural genomics.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Using a large database of protein domain families of known 3-D structure we present an analysis on the relationships among sequences, structures and functions of closely-related enzymes performed at the level of catalytic domains. Only in 38% of the pairs of homologous catalytic domains characterized by over about 60% of sequence identity the functions are almost completely identical. Nearly 43% of the pairs differ in their substrate specificity. Hence the most common variation of enzyme function among the closely-related homologues is the differences in the substrate specificity. For homologous pairs characterized by ...
Source: In Silico Biol - June 28, 2009 Category: Biology Authors: Roy A, Srinivasan N, Gowri VS Tags: In Silico Biol Source Type: journals

Mathematical modeling of regulation of type III secretion system in Salmonella enterica serovar Typhimurium by SirA.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Salmonella enterica serovar Typhimurium invades the intestinal epithelial cells using type three secretion system (TTSS) encoded on Salmonella pathogenicity island-1 (SPI-1). The key regulator of this secretion system is HilA, which is in turn regulated by HilD, HilC and RtsA. It is also known that SirA/BarA system, a two-component regulatory system plays a crucial role in regulating HilA. There are two different mechanisms that have been proposed earlier for regulation of HilD-HilC-RtsA-HilA network by SirA. One considers SirA to be acting through HilA and HilC, whereas the other considers SirA to be acting through Hi...
Source: In Silico Biol - June 28, 2009 Category: Biology Authors: Ganesh AB, Rajasingh H, Mande SS Tags: In Silico Biol Source Type: journals

Structure and mechanism of a transmission blocking vaccine candidate protein Pfs25 from P. falciparum: a molecular modeling and docking study.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we have done sequence analysis, homology modeling and docking studies of a typical member of the P25 family of ookinete surface protein, i.e. Pfs25 from Plasmodium falciparum. We have built a 3D model of Pfs25 based on the X-ray crystallographic structure of Pvs25 from Plasmodium vivax. Also we have modeled the Fv region of the malaria transmission blocking monoclonal antibody 4B7. This antibody is the transmission blocking monoclonal antibody for Pfs25 protein. Pfs25 and 4B7 scFv (single chain variable fragment only) docking results indicate that EGF domain III of the Pfs25 protein interacts with the scFv r...
Source: In Silico Biol - December 9, 2008 Category: Biology Authors: Sharma B Tags: In Silico Biol Source Type: journals

Structure and mechanism of a transmission blocking vaccine candidate protein Pfs25 from.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we have done sequence analysis, homology modeling and docking studies of a typical member of the P25 family of ookinete surface protein, i.e. Pfs25 from Plasmodium falciparum. We have built a 3D model of Pfs25 based on the X-ray crystallographic structure of Pvs25 from Plasmodium vivax. Also we have modeled the Fv region of the malaria transmission blocking monoclonal antibody 4B7. This antibody is the transmission blocking monoclonal antibody for Pfs25 protein. Pfs25 and 4B7 scFv (single chain variable fragment only) docking results indicate that EGF domain III of the Pfs25 protein interacts with the scFv r...
Source: In Silico Biol - November 29, 2008 Category: Biology Authors: Sharma B Tags: In Silico Biol Source Type: journals

A steady state model for the transcriptional regulation of filamentous growth in Saccharomyces cerevisiae.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Occurrence of multiple upstream activation sites (UASs) is a structural motif that is observed within the promoter of eukaryotic genes for coordinating gene expression. Transcriptional activation depends on the ability of transcriptional activators to bind to its specific UASs, which are kept inaccessible due to the nucleosomal organization of the chromatin. Targeting of chromatin remodeling complexes by a sequence specific transcriptional activator is shown to be detrimental for transcriptional initiation. Here, we analyze such a regulatory structure involving ordered recruitment of transcriptional activators and chro...
Source: In Silico Biol - November 29, 2008 Category: Biology Authors: Vinod PK, Venkatesh KV Tags: In Silico Biol Source Type: journals

PredictBias: a server for the identification of genomic and pathogenicity islands in prokaryotes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Pathogenicity Islands (PAIs) are the sub-sets of Genomic Islands (GIs) that are acquired by horizontal gene transfer (HGT) and are generally shown to have a significant deviation in G+C, dinucleotide or codon frequency from core genome. Major approaches used for PAI identification are based on composition bias and/or similarity with known PAIs. These approaches either limit the search to GIs or to regions similar to previously annotated PAIs. PredictBias is a web application for the identification of genomic and pathogenicity islands in prokaryotes based on composition bias, presence of insertion elements, proximity wi...
Source: In Silico Biol - November 29, 2008 Category: Biology Authors: Pundhir S, Vijayvargiya H, Kumar A Tags: In Silico Biol Source Type: journals

A data integration approach to predict host-pathogen protein-protein interactions: application to recognize protein interactions between human and a malarial parasite.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present a simple and generally applicable bioinformatics approach for the analysis of possible interactions between the proteins of a parasite, Plasmodium falciparum, and human host. In the first step, the physically compatible interactions between the parasite and human proteins are recognized using homology detection. This dataset of putative in vitro interactions is combined with large-scale datasets of expression and sub-cellular localization. This integrated approach reduces drastically the number of false positives and hence can be used for generating testable hypotheses. We could recognize known interactions prev...
Source: In Silico Biol - November 29, 2008 Category: Biology Authors: Krishnadev O, Srinivasan N Tags: In Silico Biol Source Type: journals

In silico comparison of real-time PCR probes for detection of pathogens.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Rapid diagnostics and risk assessment of the pathogens is possible by Real-Time Polymerase Chain Reaction (PCR) probes like TaqMan, Molecular Beacon (MB) and FRET. However, validation of such probes for real-life samples is an expensive and time consuming proposition. Hence, development and comparison of real-time probes in silico can be the first step in selection of most appropriate probe chemistry. The virulence genes specific for a model pathogen, Escherichia coli O157:H7, transmitted worldwide by contaminated water and food, were chosen to compare probe chemistries. MB was observed to be the best probe chemistry f...
Source: In Silico Biol - November 29, 2008 Category: Biology Authors: Ram S, Singh RL, Shanker R Tags: In Silico Biol Source Type: journals

Influence of C-H...pi hydrogen bonds in interleukins.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We have explored the roles played by C-H...pi hydrogen bonds in interleukins. Main-chain to side-chain C-H...pi interactions are the predominant type of interactions in interleukins. There was an average of 15 C-H...pi interactions per protein and also there was an average of one significant C-H...pi interaction for every 14 residues in the interleukins investigated. Significant contribution to C-H...pi interactions was only from Asp, Gly, His, Lys, Phe, Pro, Ser, Thr, Trp and Tyr in interleukins. Trp contributed both donor and acceptor atoms in main-chain to side-chain, main-chain to side-chain 5 member aromatic ring ...
Source: In Silico Biol - November 29, 2008 Category: Biology Authors: Anand S, Anbarasu A, Sethumadhavan R Tags: In Silico Biol Source Type: journals

Docking-MM-GB/SA and ADME screening of HIV-1 NNRTI inhibitor: Nevirapine and its analogues.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Nevirapine and its synthetic analogues, a class of non-nucleoside inhibitors (NNRTIs) of HIV-1 reverse transcriptase (RT), have been the objective of numerous studies focused to prepare better and safer anti-HIV drugs. We developed a library of nevirapine analogues (47) using combinatorial design and with structural modification at X, Y and R substituents in the parent structure of nevirapine. Their molecular interactions and binding affinities with reverse transcriptase (3HVT and 1VRT) have been studied using the docking-molecular mechanics based generalized Born/surface area (MM-GB/SA) solvation model. Final screenin...
Source: In Silico Biol - November 29, 2008 Category: Biology Authors: Sengupta D, Verma D, Naik PK Tags: In Silico Biol Source Type: journals

Computational prediction of candidate miRNAs and their targets from Medicago truncatula non-protein-coding transcripts.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Identification and analysis of miRNAs enhances our understanding of the important roles that small RNAs play in complex regulatory networks. It is often difficult to perform large-scale validation of miRNA expression that is predicted from genomic regions. Expressed transcripts provide an alternative resource to facilitate identification of miRNAs and their targets. We developed a computational pipeline to scan for miRNA genes from polyadenylated transcripts that were associated with limited protein coding potentials, corresponding to the intergenic regions of Medicago truncatula genomic sequences. Each predicted miRNA...
Source: In Silico Biol - November 29, 2008 Category: Biology Authors: Wen J, Frickey T, Weiller GF Tags: In Silico Biol Source Type: journals

Sequence and structural analyses of interleukin-8-like chemokine superfamily.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Interleukin-8 and related chemokines are small proteins that bind to receptors belonging to the large family of G-protein-coupled receptors. They can cause migration of cells like neutrophils and eosinophils and some of them are implicated in angiogenic diseases. More than 40 subfamilies of these ligands are known that share poor sequence similarity and display receptor specificity. There is very little structural information about the mode of binding between ligands and the receptors. We have employed multi-fold sensitive sequence search methods to provide a repertoire of 252 putative interleukin-8 proteins and homolo...
Source: In Silico Biol - November 29, 2008 Category: Biology Authors: Kanagarajadurai K, Sowdhamini R Tags: In Silico Biol Source Type: journals

In silico identification of putative drug targets from different metabolic pathways of Aeromonas hydrophila.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Aeromonas hydrophila is a major pathogen both of aquatic and terrestrial organisms, including humans. Infection with A. hydrophila results in severe economic losses to the aquaculture industry. In humans, Aeromonas hydrophila infections are known to cause gastroenteritis and wound infections. Investigations for developing a potential vaccine for its control are underway. The availability of the complete sequence information of A. hydrophila strain ATCC 7966T genome has made it possible to carry out the in silico analysis of its genome for various aspects of its biology. Keeping in view the possible risks that A. hydrop...
Source: In Silico Biol - November 29, 2008 Category: Biology Authors: Sharma V, Gupta P, Dixit A Tags: In Silico Biol Source Type: journals

PRIMe: a Web site that assembles tools for metabolomics and transcriptomics.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PRIMe (http://prime.psc.riken.jp/), the Platform for RIKEN Metabolomics, is a Web site that has been designed and implemented to support research and analysis workflows ranging from metabolome to transcriptome analysis. The site provides access to a growing collection of standardized measurements of metabolites obtained by using NMR, GC-MS, LC-MS, and CE-MS, and metabolomics tools that support related analyses (SpinAssign for the identification of metabolites by means of NMR, KNApSAcK for searches within metabolite databases). In addition, the transcriptomics tools provide Correlated Gene Search, and Cluster Cutting fo...
Source: In Silico Biol - November 29, 2008 Category: Biology Authors: Akiyama K, Chikayama E, Yuasa H, Shimada Y, Tohge T, Shinozaki K, Hirai MY, Sakurai T, Kikuchi J, Saito K Tags: In Silico Biol Source Type: journals

Identification and characterization of polyadenylation signal (PAS) variants in human genomic sequences based on modified EST clustering.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A large-scale analysis of human polyadenylation signals was carried out in silico. The most canonical AAUAAA hexamer and its 11 single-nucleotide variants that are most frequent in human genes were used to search for polyadenylation signals in the terminal sequences. Out of 18,277 poly(A) sites that were identified from 26,414 human genes, 82.5% of the sites were found to contain at least one of these 12 hexamers as a polyadenylation signal within 40 nucleotides upstream of the poly(A) site. The rest (17.5%) did not contain any of these hexamers, which suggests the existence of yet unknown signals. A total of 20,347 te...
Source: In Silico Biol - November 29, 2008 Category: Biology Authors: Kamasawa M, Horiuchi J Tags: In Silico Biol Source Type: journals

MaXlab: A novel application for the cross comparison and integration of biological signatures from microarray studies.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Microarray gene expression datasets are continually being placed in public repositories. As a result, one of the most important emerging challenges is that which enables researchers to take full advantage of such previously accumulated data to discover or validate common genes in similar biological systems. In light of this we have designed the MaXlab software to not only cross-compare available array data from different laboratories but also extract further knowledge from gene expression patterns embedded within published data. More importantly MaXlab offers a flexible and automated solution applicable for microarray ...
Source: In Silico Biol - November 29, 2008 Category: Biology Authors: Khalid S, Khan M, Gorle CB, Fraser K, Wang P, Liu X, Li S Tags: In Silico Biol Source Type: journals

Bioinformatics databases and tools in virology research: an overview.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Viruses are major factors of human infectious diseases. Understanding of the structure-function correlation in viruses is important for the identification of potential anti-viral inhibitors and vaccine targets. In virology research, virus-related databases and bioinformatic analysis tools are essential for discerning relationships within complex datasets about viruses and host-virus interactions. Bioinformatic analyses on viruses include the identification of open reading frames, gene prediction, homology searching, sequence alignment, and motif and epitope recognition. The predictions of features such as transmembrane...
Source: In Silico Biol - October 24, 2008 Category: Biology Authors: Yan Q Tags: In Silico Biol Source Type: journals

In silico analysis of microsatellites in organellar genomes of major cereals for understanding their phylogenetic relationships.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Microsatellites are abundant across prokaryotic and eukaryotic genomes. However, comparative analysis of microsatellites in the organellar genomes of plants and their utility in understanding phylogeny has not been reported. The purpose of this study was to understand the organization of microsatellites in the coding and non-coding regions of organellar genomes of major cereals viz., rice, wheat, maize and sorghum. About 5.8-14.3% of mitochondrial and 30.5-43.2% of chloroplast microsatellites were observed in the coding regions. About 83.8-86.8% of known mitochondrial genes had at least one microsatellite while this va...
Source: In Silico Biol - October 24, 2008 Category: Biology Authors: Rajendrakumar P, Biswal AK, Balachandran SM, Sundaram RM Tags: In Silico Biol Source Type: journals

Computational identification of three-way junctions in folded RNAs: a case study in arabidopsis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Three-way junctions in folded RNAs have been investigated both experimentally and computationally. The interest in their analysis stems from the fact that they have significantly been found to possess a functional role. In recent work, three-way junctions have been categorized into families depending on the relative lengths of the segments linking the three helices. Here, based on ideas originating from computational geometry, an algorithm is proposed for detecting three-way junctions in data sets of genes that are related to a metabolic pathway of interest. In its current implementation, the algorithm relies on a movi...
Source: In Silico Biol - October 24, 2008 Category: Biology Authors: Cohen A, Bocobza S, Veksler I, Gabdank I, Barash D, Aharoni A, Shapira M, Kedem K Tags: In Silico Biol Source Type: journals

COPid: composition based protein identification.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In the past, a large number of methods have been developed for predicting various characteristics of a protein from its composition. In order to exploit the full potential of protein composition, we developed the web-server COPid to assist the researchers in annotating the function of a protein from its composition using whole or part of the protein. COPid has three modules called search, composition and analysis. The search module allows searching of protein sequences in six different databases. Search results list database proteins in ascending order of Euclidian distance or descending order of compositional similari...
Source: In Silico Biol - October 24, 2008 Category: Biology Authors: Kumar M, Thakur V, Raghava GP Tags: In Silico Biol Source Type: journals

A machine learning based method for the prediction of secretory proteins using amino acid composition, their order and similarity-search.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, a systematic attempt has been made to predict secretory proteins irrespective of presence or absence of N-terminal signal peptides (also known as classical and non-classical secreted proteins respectively), using machine-learning techniques; artificial neural network (ANN) and support vector machine (SVM). We trained and tested our methods on a dataset of 3321 secretory and 3654 non-secretory mammalian proteins using five-fold cross-validation technique. First, ANN-based modules have been developed for predicting secretory proteins using 33 physico-chemical properties, amino acid composition and dipeptide co...
Source: In Silico Biol - October 24, 2008 Category: Biology Authors: Garg A, Raghava GP Tags: In Silico Biol Source Type: journals

Vector-G: multi-modular SVM-based heterotrimeric G protein prediction.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present here a robust computational method for finding new G proteins and their homologs using a SVM based pattern recognition algorithm. Several physicochemical and compositional properties including dipeptide, tripeptide and hydrophobicity composition are used for generating the SVM classifiers. This method has 96.17%, 95.38%, 97.6% sensitivity and 99.45%, 100%, 100% specificity on test sets for G protein alpha, beta, and gamma subunits, respectively. This algorithm correctly predicts the known alpha, beta and gamma subunits reported in literature. One important contribution of this algorithm is that it helps in impro...
Source: In Silico Biol - October 24, 2008 Category: Biology Authors: Jain P, Wadhwa P, Aygun R, Podila G Tags: In Silico Biol Source Type: journals

Constraint-based knowledge discovery from SAGE data.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Current analyses of co-expressed genes are often based on global approaches such as clustering or bi-clustering. An alternative way is to employ local methods and search for patterns--sets of genes displaying specific expression properties in a set of situations. The main bottleneck of this type of analysis is twofold--computational costs and an overwhelming number of candidate patterns which can hardly be further exploited. A timely application of background knowledge available in literature databases, biological ontologies and other sources can help to focus on the most plausible patterns only. The paper proposes, im...
Source: In Silico Biol - October 24, 2008 Category: Biology Authors: Klémal J, Blachon S, Soulet A, Crémilleux B, Gandrillon O Tags: In Silico Biol Source Type: journals

ROSY--a flexible and universal database and bioinformatics tool platform for Roseobacter related species.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Systems biology approaches to bacteria require an integrated database and a bioinformatics tool platform to enable automated and manual annotation, regulatory and metabolic network deduction, and the storage of related experimental as well as predicted data. In this context ROSY--the Roseobacter SYstems biology database--was developed for completed and draft genomes of representatives of the marine Roseobacter clade, which constitutes one of the most abundant bacterial clades in the ocean. ROSY provides an integrative view on comprehensive data collections such as KEGG, GenBank, RoseoBase, BRENDA, and PRODORIC as well ...
Source: In Silico Biol - October 24, 2008 Category: Biology Authors: Pommerenke C, Gabriel I, Bunk B, Münch R, Haddad I, Tielen P, Wagner-Döbler I, Jahn D Tags: In Silico Biol Source Type: journals

GASCO: genetic algorithm simulation for codon optimization.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Codon optimization is a generic technique to achieve optimum expression of a foreign gene in the host's cell system. Selection of optimum codons depends on codon usage of the host genome and the presence of several desirable and undesirable sequence motifs. Searching these motifs in all possible combinations of the codons increases the search space exponentially with respect to sequence length. GASCO is an algorithm developed for the optimum codon selection using genetic algorithms. The algorithm reduces the search space and provides an approximate solution to the problem. The algorithm has applications in DNA vaccine ...
Source: In Silico Biol - October 24, 2008 Category: Biology Authors: Sandhu KS, Pandey S, Maiti S, Pillai B Tags: In Silico Biol Source Type: journals

An in silico Analysis of Cytochrome c from Phanerochaete chrysosporium: Its Amino Acid Sequence and Characterization of Gene Structural Elements.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
An in silico approach was used to investigate cytochrome c and the cytochrome c gene of Phanerochaete chrysosporium. The cytochrome c gene contains four introns. Omission of the introns reveals a DNA sequence coding for a complete predicted amino acid sequence for P. chrysosporium cytochrome c consistent with those of other cytochromes c. Fungal cytochromes c often have a short N-terminal peptide preceding a Gly that is the N-terminal amino acid in many cytochromes c. Thus a microexon codes for an N-terminal pentapeptide (MetProTyrAlaPro) in P. chrysosporium that is identical to the N-terminal pentapeptide of Schizosac...
Source: In Silico Biol - April 24, 2008 Category: Biology Authors: Bumpus JA, Trax M, Reisdorph A, Boyd C, Gilbert D, Techau S, Ventullo RM Tags: In Silico Biol Source Type: journals

Evolutionary Origin of the Protozoan Parasites Histone-like Proteins (HU).Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The histone-like proteins (HU) belong to a family of DNA architectural proteins that stabilize nucleoprotein complexes. We found a putative HU protein (TgGlmHMM_3045) in Toxoplasma gondii genome that was homologous to the bacterial HU protein. This putative sequence was located in the scaffold TGG_995361 of the chromosome 10. The sequence included the prokaryotic bacterial histone-like domain, KFGSLGlRRRGERVARNPRT (ID number PS00045). HU protein sequences were also found in Plasmodium falciparum, Neospora caninum, Theileria parva and Theileria annulata. We found that the homology of the putative HU protein in Apicomple...
Source: In Silico Biol - April 24, 2008 Category: Biology Authors: Arenas AF, Escobar AJ, Gómez-Marin JE Tags: In Silico Biol Source Type: journals

The GTP Binding Sites Interacted with RNA-Dependent RNA Polymerase of Classical Swine Fever Virus in de novo Initiation.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The NS5B protein of classical swine fever virus (CSFV) is an important enzyme bearing a unique RNA-dependent RNA polymerase (RdRp) activity. The RdRp plays a crucial role in the viral replication cycle and in forming a replicase complex. However, the initiating synthesis mechanism of the CSFV RNA polymerase is unclearly described at present. Our aim is to reveal the RdRp-GTP docking sites and the effective modules of GTP initially bound to the polymerase in starting initiation of replication according to a well predicted CSFV RdRp model. Based on some known crystal structures of RNA polymerase, computational methods we...
Source: In Silico Biol - April 24, 2008 Category: Biology Authors: Xu Z, Chao Y, Si Y, Wang J, Jin M, Guo A, Qian P, Zhou R, Chen H Tags: In Silico Biol Source Type: journals

Distinct patterns in the regulation and evolution of human cancer genes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Understanding the mechanism of regulation of cancer genes and the constraints on their coding sequences is of fundamental importance in understanding the process of tumour development. Here we test the hypothesis that tumour suppressor genes and proto-oncogenes, due to their involvement in tumourigenesis, have distinct patterns of regulation and coding selective constraints compared to non-cancer genes. Indeed, we found significantly greater conservation in the promoter regions of proto-oncogenes, suggesting that these genes are more tightly regulated, i.e. they are more likely to contain a higher density of cis-regula...
Source: In Silico Biol - April 24, 2008 Category: Biology Authors: Furney SJ, Madden SF, Kisiel TA, Higgins DG, Lopez-Bigas N Tags: In Silico Biol Source Type: journals

NetAtlas: A Cytoscape Plugin to Examine Signaling Networks Based on Tissue Gene Expression.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Graphical methods are useful for visualizing signaling networks derived from the synthesis of large bodies of literature information or large-scale experimental measurements. Software tools to filter and organize these networks allow the exploration of their inherent biological and structural properties. We have developed NetAtlas, an open-source, Java-based Cytoscape plugin for examining signaling networks in the context of tissue gene expression patterns. The tissue gene expression data available through NetAtlas consists of 79 human tissues, 61 mouse tissues, and 44 combined tissues from 3 rat strains. Users may als...
Source: In Silico Biol - April 24, 2008 Category: Biology Authors: Yang L, Walker JR, Hogenesch JB, Thomas RS Tags: In Silico Biol Source Type: journals

BioCompass: A Novel Functional Inference Tool that Utilizes MeSH Hierarchy to Analyze Groups of Genes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Microarray technology has become employed widely for biological researchers to identify genes associated with conditions such as diseases and drugs. To date, many methods have been developed to analyze data covering a large number of genes, but they focus only on statistical significance and cannot decipher the data with biological concepts. Gene Ontology (GO) is utilized to understand the data with biological interpretation; however, it is restricted to specific ontology such as biological process, molecular function, and cellular component. Here, we attempted to apply MeSH (Medical Subject Headings) to interpret grou...
Source: In Silico Biol - April 24, 2008 Category: Biology Authors: Nakazato T, Takinaka T, Mizuguchi H, Matsuda H, Bono H, Asogawa M Tags: In Silico Biol Source Type: journals

M@IA: A Modular Open-Source Application for Microarray Workflow and Integrative Datamining.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Microarray technology is a widely used approach to gene expression analysis. Many tools for microarray management and data analysis have been developed, and recently new methods have been proposed for deciphering biological pathways by integrating microarray data with other data sources. However, to improve microarray analysis and provide meaningful gene interaction networks, integrated software solutions are still needed. Therefore, we developed M@IA, an environment for DNA microarray data analysis allowing gene network reconstruction. M@IA is a microarray integrated application which includes all of the steps of a mi...
Source: In Silico Biol - April 24, 2008 Category: Biology Authors: Le Béchec A, Zindy P, Sierocinski T, Petritis D, Bihouée A, Le Meur N, Léger J, Théret N Tags: In Silico Biol Source Type: journals

Storage and annotation of reaction kinetics data. Proceedings of a workshop. Heidelberg, Germany. May 21-23, 2007.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: PMID: 17822385 [PubMed - indexed for MEDLINE] (Source: In Silico Biol)
Source: In Silico Biol - October 19, 2007 Category: Biology Tags: In Silico Biol Source Type: journals

Workshop on "storage and annotation of reaction kinetics data", Villa Bosch in Heidelberg, May 21-23, 2007.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 17822385 [PubMed - in process] (Source: In Silico Biol)
Source: In Silico Biol - September 15, 2007 Category: Biology Authors: Rojas I, Wittig U Tags: In Silico Biol Source Type: journals

Integrating pathway data for systems pathology.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The HumanPSD database on the complete proteomes of human, mouse and rat has been integrated with the databases TRANSFAC on gene regulation and TRANSPATH on signal transduction to provide a comprehensive systems biological platform for these organisms. As a next step, integration with PathoDB and PathoSign on pathologically relevant mutations is planned together with an extension beyond the limits of the individual cell, towards intercellular networks, by integrating the database EndoNet on hormonal networks as well. The overall aim is to come up with a platform that is suitable to provide knowledge for systems patholog...
Source: In Silico Biol - September 15, 2007 Category: Biology Authors: Wingender E, Hogan J, Schacherer F, Potapov AP, Kel-Margoulis O Tags: In Silico Biol Source Type: journals

Data and model integration using JWS Online.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Systems Biology requires a tight integration of experimental data and detailed computer models to obtain a quantitative understanding of the system under study. To facilitate this integration a standardization of data and model representation and storage is important. We illustrate here such an integration using JWS Online, the modeling tool developed in our group. We follow the approach of the Silicon Cell project for the construction and validation of kinetic models and discuss some issues with respect to storage of experimental data and models. The majority of the published kinetic models for biological systems have...
Source: In Silico Biol - September 15, 2007 Category: Biology Authors: van Gend C, Conradie R, du Preez FB, Snoep JL Tags: In Silico Biol Source Type: journals