Databases & Softw...
Follow
Find
3.3K views | +0 today
Scooped by Biswapriya Biswavas Misra
onto Databases & Softwares
Scoop.it!

CAT 1.0 - Composition Analysis Toolkit

CAT 1.0 - Composition Analysis Toolkit | Databases & Softwares | Scoop.it
CAT (Composition Analysis Toolkit) is a software package that includes a novel measure of codon usage bias, Codon Deviation Coefficient (CDC). ... The Zhang Lab — Computational Biology and Bioinformatics ...
more...
No comment yet.
Databases & Softwares
Genomic, Proteomic, Transcriptomic, Metabolomic Softwares and Databases
Your new post is loading...
Scooped by Biswapriya Biswavas Misra
Scoop.it!

A survey of plant and algal genomes and transcriptomes reveals new insights into the evolution and function of the cellulose synthase superfamily

Enzymes of the cellulose synthase (CesA) family and CesA-like (Csl) families are responsible for the synthesis of celluloses and hemicelluloses, and thus are of great interest to bioenergy research. We studied the occurrences and phylogenies of CesA/Csl families in diverse plants and algae by comprehensive data mining of 82 genomes and transcriptomes.
Biswapriya Biswavas Misra's insight:
Background

Enzymes of the cellulose synthase (CesA) family and CesA-like (Csl) families are responsible for the synthesis of celluloses and hemicelluloses, and thus are of great interest to bioenergy research. We studied the occurrences and phylogenies of CesA/Csl families in diverse plants and algae by comprehensive data mining of 82 genomes and transcriptomes.

Results

We found that 1) charophytic green algae (CGA) have orthologous genes in CesA, CslC and CslD families; 2) liverwort genes are found in the CesA, CslA, CslC and CslD families; 3) The fern Pteridium aquilinum not only has orthologs in these conserved families but also in the CslB, CslH and CslE families; 4) basal angiosperms, e.g. Aristolochia fimbriata, have orthologs in these families too; 5) gymnosperms have genes forming clusters ancestral to CslB/H and to CslE/J/G respectively; 6) CslG is found in switchgrass and basal angiosperms; 7) CslJ is widely present in dicots and monocots; 8) CesA subfamilies have already diversified in ferns.

Conclusions

We speculate that: (i) ferns and horsetails might both have CslH enzymes, responsible for the synthesis of mixed-linkage glucans and (ii) CslD and similar genes might be responsible for the synthesis of mannans in CGA. Our findings led to a more detailed model of cell wall evolution and suggested that gene loss played an important role in the evolution of Csl families. We also demonstrated the usefulness of transcriptome data in the study of plant cell wall evolution and diversity.

more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

openBEB: open biological experiment browser for correlative measurements

New experimental methods must be developed to study interaction networks in systems biology. To reduce biological noise, individual subjects, such as single cells, should be analyzed using high throughput approaches. The measurement of several correlative physical properties would further improve data consistency. Accordingly, a considerable quantity of data must be acquired, correlated, catalogued and stored in a database for subsequent analysis.
Biswapriya Biswavas Misra's insight:
Background

New experimental methods must be developed to study interaction networks in systems biology. To reduce biological noise, individual subjects, such as single cells, should be analyzed using high throughput approaches. The measurement of several correlative physical properties would further improve data consistency. Accordingly, a considerable quantity of data must be acquired, correlated, catalogued and stored in a database for subsequent analysis.

Results

We have developed openBEB (open Biological Experiment Browser), a software framework for data acquisition, coordination, annotation and synchronization with database solutions such as openBIS. OpenBEB consists of two main parts: A core program and a plug-in manager. Whereas the data-type independent core of openBEB maintains a local container of raw-data and metadata and provides annotation and data management tools, all data-specific tasks are performed by plug-ins. The open architecture of openBEB enables the fast integration of plug-ins, e.g., for data acquisition or visualization. A macro-interpreter allows the automation and coordination of the different modules. An update and deployment mechanism keeps the core program, the plug-ins and the metadata definition files in sync with a central repository.

Conclusions

The versatility, the simple deployment and update mechanism, and the scalability in terms of module integration offered by openBEB make this software interesting for a large scientific community. OpenBEB targets three types of researcher, ideally working closely together: (i) Engineers and scientists developing new methods and instruments, e.g., for systems-biology, (ii) scientists performing biological experiments, (iii) theoreticians and mathematicians analyzing data. The design of openBEB enables the rapid development of plug-ins, which will inherently benefit from the "house keeping" abilities of the core program. We report the use of openBEB to combine live cell microscopy, microfluidic control and visual proteomics. In this example, measurements from diverse, complementary techniques are combined and correlated.

more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

CREAL - CREAL

Biswapriya Biswavas Misra's insight:

This is a joint work with Roderic Guigó's group - Bioinformatics and Genomics program, Center for Genomic Regulatio (CRG). This R package is designed to compare transcript relative expression of different conditions obtained from RNA-seq experiments. Our approach is based on a distance-based non-parametric multivariate ANOVA method.

The Linux version of the package is currently under development at Bioconductor (http://www.bioconductor.org/).  To install a beta version of rasp, start R and enter:

source("http://www.creal.cat/media/upload/arxius/jr/CREAL_install/install.R";)

creal.install("rasp")

more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

The protein-protein interaction network of eyestalk, Y-organ and hepatopancreas in Chinese mitten crab Eriocheir sinensis

The protein-protein interaction network (PIN) is an effective information tool for understanding the complex biological processes inside the cell and solving many biological problems such as signaling pathway identification and prediction of protein functions. Eriocheir sinensis is a highly-commercial aquaculture species with an unclear proteome background which hinders the construction and development of PIN for E. sinensis. However, in recent years, the development of next-generation deep-sequencing techniques makes it possible to get high throughput data of E. sinensis tanscriptome and subsequently obtain a systematic overview of the protein-protein interaction system.
Biswapriya Biswavas Misra's insight:
Abstract (provisional)Background

The protein-protein interaction network (PIN) is an effective information tool for understanding the complex biological processes inside the cell and solving many biological problems such as signaling pathway identification and prediction of protein functions. Eriocheir sinensis is a highly-commercial aquaculture species with an unclear proteome background which hinders the construction and development of PIN for E. sinensis. However, in recent years, the development of next-generation deep-sequencing techniques makes it possible to get high throughput data of E. sinensis tanscriptome and subsequently obtain a systematic overview of the protein-protein interaction system.

Results

In this work we sequenced the transcriptional RNA of eyestalk, Y-organ and hepatopancreas in E. sinensis and generated a PIN of E. sinensis which included 3,223 proteins and 35,787 interactions. Each protein-protein interaction in the network was scored according to the homology and genetic relationship. The signaling sub-network, representing the signal transduction pathways in E. sinensis, was extracted from the global network, which depicted a global view of the signaling systems in E. sinensis. Seven basic signal transduction pathways were identified in E. sinensis. By investigating the evolution paths of the seven pathways, we found that these pathways got mature in different evolutionary stages. Moreover, the functions of unclassified proteins and unigenes in the PIN of E. sinensis were predicted. Specifically, the functions of 549 unclassified proteins related to 864 unclassified unigenes were assigned, which respectively covered 76% and 73% of all the unclassified proteins and unigenes in the network.

Conclusions

The PIN generated in this work is the first large-scale PIN of aquatic crustacean, thereby providing a paradigmatic blueprint of the aquatic crustacean interactome. Signaling sub-network extracted from the global PIN depicts the interaction of different signaling proteins and the evolutionary paths of the identified signal transduction pathways. Furthermore, the function assignment of unclassified proteins based on the PIN offers a new reference in protein function exploration. More importantly, the construction of the E. sinensis PIN provides necessary experience for the exploration of PINs in other aquatic crustacean species.

more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

Genomic tRNA Database

more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

GPMDB Proteome Database

GPMDB Proteome Database | Databases & Softwares | Scoop.it
more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

khmer 1.0

Biswapriya Biswavas Misra's insight:

The khmer team is pleased to announce the release of khmer version 1.0. khmer is our software for working efficiently with fixed length DNA words, or k-mers, for research and work in computational biology.

more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

GeneSense: a new approach for human gene annotation integrated with protein-protein interaction networks

GeneSense: a new approach for human gene annotation integrated with protein-protein interaction networks | Databases & Softwares | Scoop.it
Virtually all cellular functions involve protein-protein interactions (PPIs). As an increasing number of PPIs are identified and vast amount of information accumulated, researchers are finding different ways to interrogate the data and understand the interactions in context. However, it is widely recognized that a significant portion of the data is scattered, redundant, not considered high quality, and not readily accessible to researchers in a systematic fashion. In addition, it is challenging to identify the optimal protein targets in the current PPI networks. The GeneSense server was developed to integrate gene annotation and PPI networks in an expandable architecture that incorporates selected databases with the aim to assemble, analyze, evaluate and disseminate protein-protein association information in a comprehensive and user-friendly manner. Three network models including nodenet, leafnet and loopnet are used to identify the optimal protein targets in the complex networks. GeneSense is freely available at www.biomedsense.org/genesense.php.
Biswapriya Biswavas Misra's insight:

Virtually all cellular functions involve protein-protein interactions (PPIs). As an increasing number of PPIs are identified and vast amount of information accumulated, researchers are finding different ways to interrogate the data and understand the interactions in context. However, it is widely recognized that a significant portion of the data is scattered, redundant, not considered high quality, and not readily accessible to researchers in a systematic fashion. In addition, it is challenging to identify the optimal protein targets in the current PPI networks. The GeneSense server was developed to integrate gene annotation and PPI networks in an expandable architecture that incorporates selected databases with the aim to assemble, analyze, evaluate and disseminate protein-protein association information in a comprehensive and user-friendly manner. Three network models including nodenet, leafnet and loopnet are used to identify the optimal protein targets in the complex networks. GeneSense is freely available at www.biomedsense.org/genesense.php.

more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

PSEA: Kinase-specific prediction and analysis of human phosphorylation substrates

PSEA: Kinase-specific prediction and analysis of human phosphorylation substrates | Databases & Softwares | Scoop.it
Protein phosphorylation catalysed by kinases plays crucial regulatory roles in intracellular signal transduction. With the increasing number of kinase-specific phosphorylation sites and disease-related phosphorylation substrates that have been identified, the desire to explore the regulatory relationship between protein kinases and disease-related phosphorylation substrates is motivated. In this work, we analysed the kinases' characteristic of all disease-related phosphorylation substrates by using our developed Phosphorylation Set Enrichment Analysis (PSEA) method. We evaluated the efficiency of our method with independent test and concluded that our approach is reliable for identifying kinases responsible for phosphorylated substrates. In addition, we found that Mitogen-activated protein kinase (MAPK) and Glycogen synthase kinase (GSK) families are more associated with abnormal phosphorylation. It can be anticipated that our method might be helpful to identify the mechanism of phosphorylation and the relationship between kinase and phosphorylation related diseases. A user-friendly web interface is now freely available at http://bioinfo.ncu.edu.cn/PKPred_Home.aspx.
more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

AlgaePath: comprehensive analysis of metabolic pathways using transcript abundance data from next-generation sequencing in green algae

Algae are important non-vascular plants that have many research applications, including high species diversity, biofuel sources, and adsorption of heavy metals and, following processing, are used as ingredients in health supplements. The increasing availability of next-generation sequencing (NGS) data for algae genomes and transcriptomes has made the development of an integrated resource for retrieving gene expression data and metabolic pathway essential for functional analysis and systems biology. In a currently available resource, gene expression profiles and biological pathways are displayed separately, making it impossible to easily search current databases to identify the cellular response mechanisms. Therefore, in this work the novel AlgaePath database was developed to retrieve transcript abundance profiles efficiently under various conditions in numerous metabolic pathways.
Biswapriya Biswavas Misra's insight:
Abstract (provisional)Background

Algae are important non-vascular plants that have many research applications, including high species diversity, biofuel sources, and adsorption of heavy metals and, following processing, are used as ingredients in health supplements. The increasing availability of next-generation sequencing (NGS) data for algae genomes and transcriptomes has made the development of an integrated resource for retrieving gene expression data and metabolic pathway essential for functional analysis and systems biology. In a currently available resource, gene expression profiles and biological pathways are displayed separately, making it impossible to easily search current databases to identify the cellular response mechanisms. Therefore, in this work the novel AlgaePath database was developed to retrieve transcript abundance profiles efficiently under various conditions in numerous metabolic pathways.

Description: AlgaePath is a web-based database that integrates gene information, biological pathways, and NGS datasets for the green algae Chlamydomonas reinhardtii and Neodesmus sp. UTEX 2219-4. Users can search this database to identify transcript abundance profiles and pathway information using five query pages (Gene Search, Pathway Search, Differentially Expressed Genes (DEGs) Search, Gene Group Analysis, and Co-expression Analysis). The transcript abundance data of 45 and four samples from C. reinhardtii and Neodesmus sp. UTEX 2219-4, respectively, can be obtained directly on pathway maps. Genes that are differentially expressed between two conditions can be identified using Folds Search. The Gene Group Analysis page includes a pathway enrichment analysis, and can be used to easily compare the transcript abundance profiles of functionally related genes on a map. Finally, the Co-expression Analysis page can be used to search for co-expressed transcripts of a target gene. The results of the searches will provide a valuable reference for designing further experiments and for elucidating critical mechanisms from high-throughput data.

Conclusions

AlgaePath is an effective interface that can be used to clarify the transcript response mechanisms in different metabolic pathways under various conditions. Importantly, AlgaePath can be mined to identify critical mechanisms based on high-throughput sequencing. To our knowledge, AlgaePath is the most comprehensive resource for integrating numerous databases and analysis tools in algae. The system can be accessed freely online at http://AlgaePath.itps.ncku.edu.tw.

 
more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

BLIND ordering of large-scale transcriptomic developmental timecourses

BLIND ordering of large-scale transcriptomic developmental timecourses | Databases & Softwares | Scoop.it
Biswapriya Biswavas Misra's insight:

RNA-Seq enables the efficient transcriptome sequencing of many samples from small amounts of material, but the analysis of these data remains challenging. In particular, in developmental studies, RNA-Seq is challenged by the morphological staging of samples, such as embryos, since these often lack clear markers at any particular stage. In such cases, the automatic identification of the stage of a sample would enable previously infeasible experimental designs. Here we present the ‘basic linear index determination of transcriptomes’ (BLIND) method for ordering samples comprising different developmental stages. The method is an implementation of a traveling salesman algorithm to order the transcriptomes according to their inter-relationships as defined by principal components analysis. To establish the direction of the ordered samples, we show that an appropriate indicator is the entropy of transcriptomic gene expression levels, which increases over developmental time. Using BLIND, we correctly recover the annotated order of previously published embryonic transcriptomic timecourses for frog, mosquito, fly and zebrafish. We further demonstrate the efficacy of BLIND by collecting 59 embryos of the sponge Amphimedon queenslandica and ordering their transcriptomes according to developmental stage. BLIND is thus useful in establishing the temporal order of samples within large datasets and is of particular relevance to the study of organisms with asynchronous development and when morphological staging is difficult.

more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

RNA CoMPASS: A Dual Approach for Pathogen and Host Transcriptome Analysis of RNA-Seq Datasets

Biswapriya Biswavas Misra's insight:

High-throughput RNA sequencing (RNA-seq) has become an instrumental assay for the analysis of multiple aspects of an organism's transcriptome. Further, the analysis of a biological specimen's associated microbiome can also be performed using RNA-seq data and this application is gaining interest in the scientific community. There are many existing bioinformatics tools designed for analysis and visualization of transcriptome data. Despite the availability of an array of next generation sequencing (NGS) analysis tools, the analysis of RNA-seq data sets poses a challenge for many biomedical researchers who are not familiar with command-line tools. Here we present RNA CoMPASS, a comprehensive RNA-seq analysis pipeline for the simultaneous analysis of transcriptomes and metatranscriptomes from diverse biological specimens. RNA CoMPASS leverages existing tools and parallel computing technology to facilitate the analysis of even very large datasets. RNA CoMPASS has a web-based graphical user interface with intrinsic queuing to control a distributed computational pipeline. RNA CoMPASS was evaluated by analyzing RNA-seq data sets from 45 B-cell samples. Twenty-two of these samples were derived from lymphoblastoid cell lines (LCLs) generated by the infection of naïve B-cells with the Epstein Barr virus (EBV), while another 23 samples were derived from Burkitt's lymphomas (BL), some of which arose in part through infection with EBV. Appropriately, RNA CoMPASS identified EBV in all LCLs and in a fraction of the BLs. Cluster analysis of the human transcriptome component of the RNA CoMPASS output clearly separated the BLs (which have a germinal center-like phenotype) from the LCLs (which have a blast-like phenotype) with evidence of activated MYC signaling and lower interferon and NF-kB signaling in the BLs. Together, this analysis illustrates the utility of RNA CoMPASS in the simultaneous analysis of transcriptome and metatranscriptome data. RNA CoMPASS is freely available at http://rnacompass.sourceforge.net/.

Go to: 
more...
No comment yet.
Rescooped by Biswapriya Biswavas Misra from MycorWeb Plant-Microbe Interactions
Scoop.it!

Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction

Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction | Databases & Softwares | Scoop.it
Many microbial, fungal, or oomcyete populations violate assumptions for population genetic analysis because these populations are clonal, admixed, partially clonal, and/or sexual. Furthermore, few tools exist that are specifically designed for analyzing data from clonal populations, making analysis difficult and haphazard. We developed the R package poppr providing unique tools for analysis of data from admixed, clonal, mixed, and/or sexual populations. Currently, poppr can be used for dominant/codominant and haploid/diploid genetic data. Data can be imported from several formats including GenAlEx formatted text files and can be analyzed on a user-defined hierarchy that includes unlimited levels of subpopulation structure and clone censoring. New functions include calculation of Bruvo’s distance for microsatellites, batch-analysis of the index of association with several indices of genotypic diversity, and graphing including dendrograms with bootstrap support and minimum spanning networks. While functions for genotypic diversity and clone censoring are specific for clonal populations, several functions found in poppr are also valuable to analysis of any populations. A manual with documentation and examples is provided. Poppr is open source and major releases are available on CRAN: http://cran.r-project.org/package=poppr. More supporting documentation and tutorials can be found under ‘resources’ at: http://grunwaldlab.cgrb.oregonstate.edu/.

Via Niklaus Grunwald, Francis Martin
more...
Steve Marek's curator insight, March 6, 1:35 AM

this looks useful

Scooped by Biswapriya Biswavas Misra
Scoop.it!

READemption - A tool for the computational analysis of deep-sequencing-based transcriptome data

READemption - A tool for the computational analysis of deep-sequencing-based transcriptome data | Databases & Softwares | Scoop.it
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
Biswapriya Biswavas Misra's insight:

Summary: RNA-Seq has become a potent and widely used method to qualitatively and quantitatively study transcriptomes. In order to draw biological conclusions based on RNA-Seq data, several steps some of which are computationally intensive, have to betaken. Our READemption pipeline takes care of these individual tasks and integrates them into an easy-to-use tool with a command line interface. To leverage the full power of modern computers, most subcommands of READemption offer parallel data processing. While READemption was mainly developed for the analysis of bacterial primary transcriptomes, we have successfully applied it to analyze RNA-Seq reads from other sample types, including whole transcriptomes, RNA immunoprecipitated with proteins, not only from bacteria, but also from eukaryotes and archaea. Availability and Implementation: READemption is implemented in Python and is published under the ISC open source license. The tool and documentation is hosted at http://pythonhosted.org/READemption (DOI:10.6084/m9.figshare.977849).

more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

MetaRef

MetaRef | Databases & Softwares | Scoop.it
Biswapriya Biswavas Misra's insight:

MetaRef is a resource to comprehensively catalog and characterize clade-specific microbial genes. We identify and provide all core genes associated with all microbial species and genera with available reference genomes (final or draft). A subset of these gene families are consistently present in one or more taxonomic clades, which allows us to further indicate them as marker genes.

more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

An Algebra-Based Method for Inferring Gene Regulatory Networks

The inference of gene regulatory networks (GRNs) from system-level experimental observations is at the heart of systems biology, due to its importance for gaining insight into the complex regulatory mechanisms in cellular systems. This includes the inference of both the network topology and its dynamics. While there are many algorithms available to infer the network topology from experimental data, less emphasis has been placed on methods that incorporate time-resolved gene expression data (time series effectively to infer network dynamics. Since the network inference problem is typically underdetermined, it is important to also have the option of incorporating prior biological knowledge about the network into the process along with an effective description of the search space for dynamic models. Finally, it is important to have an understanding of how a given inference method is affected by experimental and other noise in the data used.
Biswapriya Biswavas Misra's insight:
Abstract (provisional)Background

The inference of gene regulatory networks (GRNs) from system-level experimental observations is at the heart of systems biology, due to its importance for gaining insight into the complex regulatory mechanisms in cellular systems. This includes the inference of both the network topology and its dynamics. While there are many algorithms available to infer the network topology from experimental data, less emphasis has been placed on methods that incorporate time-resolved gene expression data (time series effectively to infer network dynamics. Since the network inference problem is typically underdetermined, it is important to also have the option of incorporating prior biological knowledge about the network into the process along with an effective description of the search space for dynamic models. Finally, it is important to have an understanding of how a given inference method is affected by experimental and other noise in the data used.

Results

This paper contains a novel inference algorithm using the algebraic framework of Boolean polynomial dynamical systems (BPDS), meeting all these requirements. The algorithm takes as input time series data, including those from network perturbations, such as knock-out mutant strains and RNAi experiments. It allows for the incorporation of prior biological knowledge while being robust to significant levels of noise in the data used for inference. It uses an evolutionary algorithm for local optimization with an encoding of the mathematical models as BPDS. The BPDS framework allows an effective representation of the search space for algebraic dynamic models that improves computational performance. The algorithm is validated with both simulated and experimental microarray expression profile data. Robustness to noise is tested using a published mathematical model of the segment polarity gene network in Drosophila melanogaster. Benchmarking of the algorithm is done by a comparison with a spectrum of state-of-the-art network inference methods on data from the synthetic IRMA network to demonstrate that our method has good precision and sensitivity for the network reconstruction task, while also predicting several of the dynamic patterns present in the network.

Conclusions

Boolean polynomial dynamical systems provide a powerful modeling framework for the reverse engineering of gene regulatory networks, that enables a rich mathematical structure on the model search space. Availability: A C++ implementation of the method, distributed under LPGL license, is available, together with the source code, at http://www.paola-vera-licona.net/Software/EARevEng/REACT.html.

more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

TSSAR: TSS annotation regime for dRNA-seq data

Differential RNA sequencing (dRNA-seq) is a high-throughput screening technique designed to examine
Biswapriya Biswavas Misra's insight:
Background

Differential RNA sequencing (dRNA-seq) is a high-throughput screening technique designed to examine the architecture of bacterial operons in general and the precise position of transcription start sites (TSS) in particular. Hitherto, dRNA-seq data were analyzed by visualizing the sequencing reads mapped to the reference genome and manually annotating reliable positions. This is very labor intensive and, due to the subjectivity, biased.

Results

Here, we present TSSAR, a tool for automated de novo TSS annotation from dRNA-seq data that respects the statistics of dRNA-seq libraries. TSSAR uses the premise that the number of sequencing reads starting at a certain genomic position within a transcriptional active region follows a Poisson distribution with a parameter that depends on the local strength of expression. The differences of two dRNA-seq library counts thus follow a Skellam distribution. This provides a statistical basis to identify significantly enriched primary transcripts.

Conclusions

Having an automated and efficient tool for analyzing dRNA-seq data facilitates the use of the dRNA-seq technique and promotes its application to more sophisticated analysis. For instance, monitoring the plasticity and dynamics of the transcriptomal architecture triggered by different stimuli and growth conditions becomes possible.

The main asset of a novel tool for dRNA-seq analysis that reaches out to a broad user community is usability. As such, we provide TSSAR both as intuitive RESTfulWeb service (http://rna.tbi.univie.ac. at/TSSAR) together with a set of post-processing and analysis tools, as well as a stand-alone version for use in high-throughput dRNA-seq data analysis pipelines.

more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

InvFEST, a database integrating information of polymorphic inversions in the human genome

InvFEST, a database integrating information of polymorphic inversions in the human genome | Databases & Softwares | Scoop.it
Biswapriya Biswavas Misra's insight:

The newest genomic advances have uncovered an unprecedented degree of structural variation throughout genomes, with great amounts of data accumulating rapidly. Here we introduce InvFEST (http://invfestdb.uab.cat), a database combining multiple sources of information to generate a complete catalogue of non-redundant human polymorphic inversions. Due to the complexity of this type of changes and the underlying high false-positive discovery rate, it is necessary to integrate all the available data to get a reliable estimate of the real number of inversions. InvFEST automatically merges predictions into different inversions, refines the breakpoint locations, and finds associations with genes and segmental duplications. In addition, it includes data on experimental validation, population frequency, functional effects and evolutionary history. All this information is readily accessible through a complete and user-friendly web report for each inversion. In its current version, InvFEST combines information from 34 different studies and contains 1092 candidate inversions, which are categorized based on internal scores and manual curation. Therefore, InvFEST aims to represent the most reliable set of human inversions and become a central repository to share information, guide future studies and contribute to the analysis of the functional and evolutionary impact of inversions on the human genome.

more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

A web server for protein-protein interaction network querying

Molecular interactions need to be taken into account to adequately model the complex behavior of
Biswapriya Biswavas Misra's insight:
Abstract (provisional)Background

Molecular interactions need to be taken into account to adequately model the complex behavior of biological systems. These interactions are captured by various types of biological networks, such as metabolic, gene-regulatory, signal transduction and protein-protein interaction networks. We recently developed NATALIE, which computes high-quality network alignments via advanced methods from combinatorial optimization.

Results

Here, we present NATALIEQ, a web server for topology-based alignment of a specified query protein-protein interaction network to a selected target network using the NATALIE algorithm. By incorporating similarity at both the sequence and the network level, we compute alignments that allow for the transfer of functional annotation as well as for the prediction of missing interactions. We illustrate the capabilities of NATALIEQ with a biological case study involving the Wnt signaling pathway.

Conclusions

We show that topology-based network alignment can produce results complementary to those obtained by using sequence similarity alone. We also demonstrate that NATALIEQ is able to predict putative interactions. The server is available at: http://www.ibi.vu.nl/programs/natalieq/.

 
more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

GeneScissors – Detecting and Correcting Spurious Transcriptome Inference due to RNAseq reads misalignment

GeneScissors – Detecting and Correcting Spurious Transcriptome Inference due to RNAseq reads misalignment | Databases & Softwares | Scoop.it
GeneScissors :: DESCRIPTION GeneScissors is a comprehensive approach to detecting and correcting spurious transcriptome inference due to RNAseq reads misalignment ::DEVELOPER Wei Wang :: SCREENSHOTS N/A (CT @rnomics/bioinfo GeneScissors...
more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

Alignment-free Visualization of Metagenomic Data by Nonlinear Dimension Reduction

Alignment-free Visualization of Metagenomic Data by Nonlinear Dimension Reduction | Databases & Softwares | Scoop.it
The visualization of metagenomic data, especially without prior taxonomic identification of reconstructed genomic fragments, is a challenging problem in computational biology. An ideal visualization method should, among others, enable clear distinction of congruent groups of sequences of closely related taxa, be applicable to fragments of lengths typically achievable following assembly, and allow the efficient analysis of the growing amounts of community genomic sequence data. Here, we report a scalable approach for the visualization of metagenomic data that is based on nonlinear dimension reduction via Barnes-Hut Stochastic Neighbor Embedding of centered log-ratio transformed oligonucleotide signatures extracted from assembled genomic sequence fragments. The approach allows for alignment-free assessment of the data-inherent taxonomic structure, and it can potentially facilitate the downstream binning of genomic fragments into uniform clusters reflecting organismal origin. We demonstrate the performance of our approach by visualizing community genomic sequence data from simulated as well as groundwater, human-derived and marine microbial communities.
more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

A pipeline for the de novo assembly of the Themira biloba (Sepsidae: Diptera) transcriptome using a multiple k-mer length approach

The Sepsidae family of flies is a model for investigating how sexual selection shapes courtship and sexual dimorphism in a comparative framework. However, like many non-model systems, there are few molecular resources available. Large-scale sequencing and assembly have not been performed in any sepsid, and the lack of a closely related genome makes investigation of gene expression challenging. Our goal was to develop an automated pipeline for de novo transcriptome assembly, and to use that pipeline to assemble and analyze the transcriptome of the sepsid Themira biloba.
Biswapriya Biswavas Misra's insight:
AbstractBackground

The Sepsidae family of flies is a model for investigating how sexual selection shapes courtship and sexual dimorphism in a comparative framework. However, like many non-model systems, there are few molecular resources available. Large-scale sequencing and assembly have not been performed in any sepsid, and the lack of a closely related genome makes investigation of gene expression challenging. Our goal was to develop an automated pipeline for de novo transcriptome assembly, and to use that pipeline to assemble and analyze the transcriptome of the sepsid Themira biloba.

Results

Our bioinformatics pipeline uses cloud computing services to assemble and analyze the transcriptome with off-site data management, processing, and backup. It uses a multiple k-mer length approach combined with a second meta-assembly to extend transcripts and recover more bases of transcript sequences than standard single k-mer assembly. We used 454 sequencing to generate 1.48 million reads from cDNA generated from embryo, larva, and pupae of T. biloba and assembled a transcriptome consisting of 24,495 contigs. Annotation identified 16,705 transcripts, including those involved in embryogenesis and limb patterning. We assembled transcriptomes from an additional three non-model organisms to demonstrate that our pipeline assembled a higher-quality transcriptome than single k-mer approaches across multiple species.

Conclusions

The pipeline we have developed for assembly and analysis increases contig length, recovers unique transcripts, and assembles more base pairs than other methods through the use of a meta-assembly. The T. biloba transcriptome is a critical resource for performing large-scale RNA-Seq investigations of gene expression patterns, and is the first transcriptome sequenced in this Dipteran family.

more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

Kraken: ultrafast metagenomic sequence classification using exact alignments

Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed for this task have been relatively slow and computationally expensive, forcing researchers to use faster abundance estimation programs, which only classify small subsets of metagenomic data. Using exact alignment of k-mers, Kraken achieves classification accuracy comparable to the fastest BLAST program. In its fastest mode, Kraken classifies 100 base pair reads at a rate of over 4.1 million reads per minute, 909 times faster than Megablast and 11 times faster than the abundance estimation program MetaPhlAn. Kraken is available at http://ccb.jhu.edu/software/kraken/.
Biswapriya Biswavas Misra's insight:

Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed for this task have been relatively slow and computationally expensive, forcing researchers to use faster abundance estimation programs, which only classify small subsets of metagenomic data. Using exact alignment of k-mers, Kraken achieves classification accuracy comparable to the fastest BLAST program. In its fastest mode, Kraken classifies 100 base pair reads at a rate of over 4.1 million reads per minute, 909 times faster than Megablast and 11 times faster than the abundance estimation program MetaPhlAn. Kraken is available at http://ccb.jhu.edu/software/kraken/.

more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

OncoFinder, a new method for the analysis of intracellular signaling pathway activation using transcriptomic data | Bioinformatics and Computational Biology

OncoFinder, a new method for the analysis of intracellular signaling pathway activation using transcriptomic data
more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

Insecticidal activity of menthol derivatives against mosquitoes

Insecticidal activity of menthol derivatives against mosquitoes | Databases & Softwares | Scoop.it
Biswapriya Biswavas Misra's insight:
Abstract

BACKGROUND: The insecticidal activity of essential oil of Mentha piperita L. emend. Huds. against local mosquitoes as disease vectors was recognized and found to be due to the presence of menthol, which is the major aroma compound of the oil. The minor compounds of the oil, i.e. menthone, β-caryophyllene, menthyl acetate, limonene, α-pinene and pulegone, showed either less or no activity against the mosquitoes tested. L-Menthol derivatives were synthesized and their knockdown effect and mortality were evaluated against local mosquitoes of Culex quinquefasciatus Say, Aedes aegypti L. and Anopheles tessellatus Theobald as disease vectors. This is the first report of mosquitocidal activity of menthol and its derivatives against Cx. quinquefasciatus, Ae. aegypti and An. tessellatus.

RESULTS: Derivative synthesis followed by structure–activity relationship studies identified several derivatives, i.e. menthyl chloroacetate, menthyl dichloroacetate, menthyl cinnamate, menthone glyceryl acetal, thymol, α-terpineol and mugetanol, with enhanced mosquitocidal activity against Cx. quinquefasciatus, Ae. aegypti and An. tessellatus relative to the parent compound L-menthone.

CONCLUSION: In ester derivatives of L-menthol the optimum activity is dependent on the size and shape of the ester group and the presence of chlorine atoms in the ester group. In structurally related derivatives of L-menthol the optimum activity is dependent on the aromaticity, the degree of unsaturation, the position of the hydroxy group and the type of functional group. Copyright © 2007 Society of Chemical Industry

more...
No comment yet.