scholarly journals novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model

2020 ◽  
Vol 48 (W1) ◽  
pp. W477-W487 ◽  
Author(s):  
Shaozhen Ding ◽  
Yu Tian ◽  
Pengli Cai ◽  
Dachuan Zhang ◽  
Xingxiang Cheng ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Web Server ◽  
Value Added ◽  
Enzyme Promiscuity ◽  
Rule Based ◽  
Target Molecule ◽  
Arduous Task ◽  
Pathway Length ◽  
User Friendly ◽  
Thermodynamic Feasibility

Abstract To increase the number of value-added chemicals that can be produced by metabolic engineering and synthetic biology, constructing metabolic space with novel reactions/pathways is crucial. However, with the large number of reactions that existed in the metabolic space and complicated metabolisms within hosts, identifying novel pathways linking two molecules or heterologous pathways when engineering a host to produce a target molecule is an arduous task. Hence, we built a user-friendly web server, novoPathFinder, which has several features: (i) enumerate novel pathways between two specified molecules without considering hosts; (ii) construct heterologous pathways with known or putative reactions for producing target molecule within Escherichia coli or yeast without giving precursor; (iii) estimate novel pathways with considering several categories, including enzyme promiscuity, Synthetic Complex Score (SCScore) and LD50 of intermediates, overall stoichiometric conversions, pathway length, theoretical yields and thermodynamic feasibility. According to the results, novoPathFinder is more capable to recover experimentally validated pathways when comparing other rule-based web server tools. Besides, more efficient pathways with novel reactions could also be retrieved for further experimental exploration. novoPathFinder is available at http://design.rxnfinder.org/novopathfinder/.

scholarly journals mCSM-membrane: predicting the effects of mutations on transmembrane proteins

2020 ◽  
Vol 48 (W1) ◽  
pp. W147-W153 ◽  
Author(s):  
Douglas E V Pires ◽  
Carlos H M Rodrigues ◽  
David B Ascher
Keyword(s):  
Membrane Proteins ◽  
Single Point ◽  
Point Mutations ◽  
Web Server ◽  
Protein Coding ◽  
Pathogenic Variants ◽  
Model Protein ◽  
Matthew’S Correlation Coefficient ◽  
Membrane Protein Stability ◽  
User Friendly

Abstract Significant efforts have been invested into understanding and predicting the molecular consequences of mutations in protein coding regions, however nearly all approaches have been developed using globular, soluble proteins. These methods have been shown to poorly translate to studying the effects of mutations in membrane proteins. To fill this gap, here we report, mCSM-membrane, a user-friendly web server that can be used to analyse the impacts of mutations on membrane protein stability and the likelihood of them being disease associated. mCSM-membrane derives from our well-established mutation modelling approach that uses graph-based signatures to model protein geometry and physicochemical properties for supervised learning. Our stability predictor achieved correlations of up to 0.72 and 0.67 (on cross validation and blind tests, respectively), while our pathogenicity predictor achieved a Matthew's Correlation Coefficient (MCC) of up to 0.77 and 0.73, outperforming previously described methods in both predicting changes in stability and in identifying pathogenic variants. mCSM-membrane will be an invaluable and dedicated resource for investigating the effects of single-point mutations on membrane proteins through a freely available, user friendly web server at http://biosig.unimelb.edu.au/mcsm_membrane.

scholarly journals Re-introduction of endogenous pathways for propionyl-CoA, 1-propanol and propionate formation in Escherichia coli

2021 ◽  
Author(s):  
Thai Le
Keyword(s):  
Escherichia Coli ◽  
Value Added ◽  
Degradation Process ◽  
Short Commentary ◽  
Chain Compounds ◽  
Propionate Formation

In a previous study, we found that 2-ketobutyrate (2-KB) was seriously degraded in Escherichia coli. In the present investigation, we tried to clarify the products of that degradation process, and intriguingly reconfirmed that 2-KB is chopped up to form propionyl-CoA, 1-propanol and propionate. This short commentary re-introduces efficient endogenous pathways for production of value-added odd-chain compounds such as propionyl-CoA-derived chemicals.

iDNA6mA-Rice-DL: A local web server for identifying DNA N6-methyladenine sites in rice genome by deep learning method

2021 ◽  
pp. 2150019
Author(s):  
Shiqian He ◽  
Liang Kong ◽  
Jing Chen
Keyword(s):  
Deep Learning ◽  
Characteristic Curve ◽  
Rice Genome ◽  
Web Server ◽  
Learning Method ◽  
Independent Dataset ◽  
Intelligent Computing ◽  
Proposed Model ◽  
Genomic Scale ◽  
User Friendly

Accurate detection of N6-methyladenine (6mA) sites by biochemical experiments will help to reveal their biological functions, still, these wet experiments are laborious and expensive. Therefore, it is necessary to introduce a powerful computational model to identify the 6mA sites on a genomic scale, especially for plant genomes. In view of this, we proposed a model called iDNA6mA-Rice-DL for the effective identification of 6mA sites in rice genome, which is an intelligent computing model based on deep learning method. Traditional machine learning methods assume the preparation of the features for analysis. However, our proposed model automatically encodes and extracts key DNA features through an embedded layer and several groups of dense layers. We use an independent dataset to evaluate the generalization ability of our model. An area under the receiver operating characteristic curve (auROC) of 0.98 with an accuracy of 95.96% was obtained. The experiment results demonstrate that our model had good performance in predicting 6mA sites in the rice genome. A user-friendly local web server has been established. The Docker image of the local web server can be freely downloaded at https://hub.docker.com/r/his1server/idna6ma-rice-dl .

scholarly journals OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species

2019 ◽  
Vol 47 (W1) ◽  
pp. W52-W58 ◽  
Author(s):  
Ling Xu ◽  
Zhaobin Dong ◽  
Lu Fang ◽  
Yongjiang Luo ◽  
Zhaoyuan Wei ◽  
...  
Keyword(s):  
Web Server ◽  
Venn Diagram ◽  
Orthologous Group ◽  
Genome Comparison ◽  
Species Number ◽  
Whole Genome ◽  
Functional Annotations ◽  
Occurrence Pattern ◽  
Multiple Species ◽  
User Friendly

Abstract OrthoVenn is a powerful web platform for the comparison and analysis of whole-genome orthologous clusters. Here we present an updated version, OrthoVenn2, which provides new features that facilitate the comparative analysis of orthologous clusters among up to 12 species. Additionally, this update offers improvements to data visualization and interpretation, including an occurrence pattern table for interrogating the overlap of each orthologous group for the queried species. Within the occurrence table, the functional annotations and summaries of the disjunctions and intersections of clusters between the chosen species can be displayed through an interactive Venn diagram. To facilitate a broader range of comparisons, a larger number of species, including vertebrates, metazoa, protists, fungi, plants and bacteria, have been added in OrthoVenn2. Finally, a stand-alone version is available to perform large dataset comparisons and to visualize results locally without limitation of species number. In summary, OrthoVenn2 is an efficient and user-friendly web server freely accessible at https://orthovenn2.bioinfotoolkits.net.

scholarly journals Production of Glucaric Acid from a Synthetic Pathway in Recombinant Escherichia coli

2008 ◽  
Vol 75 (3) ◽  
pp. 589-595 ◽  
Author(s):  
Tae Seok Moon ◽  
Sang-Hwal Yoon ◽  
Amanda M. Lanza ◽  
Joseph D. Roy-Mayhew ◽  
Kristala L. Jones Prather
Keyword(s):  
Escherichia Coli ◽  
Pseudomonas Syringae ◽  
Glucuronic Acid ◽  
Value Added ◽  
Culture Broth ◽  
Glucaric Acid ◽  
Synthetic Pathway ◽  
Genes Encoding ◽  
Microbial System ◽  
Rate Limiting

ABSTRACT A synthetic pathway has been constructed for the production of glucuronic and glucaric acids from glucose in Escherichia coli. Coexpression of the genes encoding myo-inositol-1-phosphate synthase (Ino1) from Saccharomyces cerevisiae and myo-inositol oxygenase (MIOX) from mice led to production of glucuronic acid through the intermediate myo-inositol. Glucuronic acid concentrations up to 0.3 g/liter were measured in the culture broth. The activity of MIOX was rate limiting, resulting in the accumulation of both myo-inositol and glucuronic acid as final products, in approximately equal concentrations. Inclusion of a third enzyme, uronate dehydrogenase (Udh) from Pseudomonas syringae, facilitated the conversion of glucuronic acid to glucaric acid. The activity of this recombinant enzyme was more than 2 orders of magnitude higher than that of Ino1 and MIOX and increased overall flux through the pathway such that glucaric acid concentrations in excess of 1 g/liter were observed. This represents a novel microbial system for the biological production of glucaric acid, a “top value-added chemical” from biomass.

scholarly journals An improved molecular tool for screening bacterial colonies using GFP expression enhanced by a Dictyostelium sequence

BioTechniques ◽  
2020 ◽  
Vol 68 (2) ◽  
pp. 91-95 ◽  
Author(s):  
Tomo Kondo ◽  
Shigehiko Yumura
Keyword(s):  
Escherichia Coli ◽  
Gene Sequence ◽  
Fluorescent Protein ◽  
Gfp Expression ◽  
Magnetospirillum Gryphiswaldense ◽  
E Coli ◽  
Molecular Tool ◽  
Visual Confirmation ◽  
Green Fluorescent ◽  
User Friendly

During molecular cloning, screening bacterial transformants is a time-consuming and labor-intensive process; however, tractable tools that can be applied to various vectors for visual confirmation of desired colonies are limited. Recently, we reported that translational enhancement by a Dictyostelium gene sequence (TED) boosted protein expression even without an expression inducer in Escherichia coli. Here, we demonstrate a generally applicable molecular tool using the expression of green fluorescent protein enhanced by TED. By inserting a module related to TED into the cloning site in advance, we effectively screened E. coli colonies harboring the desired plasmid functions in a prokaryote ( Magnetospirillum gryphiswaldense) or eukaryote ( Dictyostelium discoideum). Thus, our system represents a user-friendly technique for cloning.

scholarly journals JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison

2015 ◽  
Vol 32 (6) ◽  
pp. 929-931 ◽  
Author(s):  
Michael Richter ◽  
Ramon Rosselló-Móra ◽  
Frank Oliver Glöckner ◽  
Jörg Peplies
Keyword(s):  
Draft Genome ◽  
Web Server ◽  
Supplementary Information ◽  
Genome Comparison ◽  
Reference Database ◽  
Online Service ◽  
Genome Sequences ◽  
Species Circumscription ◽  
Correlation Search ◽  
User Friendly

Abstract Summary: JSpecies Web Server (JSpeciesWS) is a user-friendly online service for in silico calculating the extent of identity between two genomes, a parameter routinely used in the process of polyphasic microbial species circumscription. The service measures the average nucleotide identity (ANI) based on BLAST+ (ANIb) and MUMmer (ANIm), as well as correlation indexes of tetra-nucleotide signatures (Tetra). In addition, it provides a Tetra Correlation Search function, which allows to rapidly compare selected genomes against a continuously updated reference database with currently about 32 000 published whole and draft genome sequences. For comparison, own genomes can be uploaded and references can be selected from the JSpeciesWS reference database. The service indicates whether two genomes share genomic identities above or below the species embracing thresholds, and serves as a fast way to allocate unknown genomes in the frame of the hitherto sequenced species. Availability and implementation: JSpeciesWS is available at http://jspecies.ribohost.com/jspeciesws. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: [email protected]

The use of a rule-based module as a decision support system for dystocia detection in dairy cows

2018 ◽  
Author(s):  
D. Zaborski ◽  
W. Grzesiak ◽  
J. Wojcik
Keyword(s):  
Decision Support ◽  
Dairy Cows ◽  
Predictive Performance ◽  
Test Set ◽  
Rule Based ◽  
Black And White ◽  
Holstein Friesian ◽  
Independent Test ◽  
Tree Models ◽  
User Friendly

The aim of the present study was to construct a rule-based module (RBM) for dystocia detection in dairy cattle and to verify its predictive performance. A total of 3041 calving records of Polish Holstein-Friesian Black-and-White heifers and cows were used. Three continuous and seven categorical predictors of dystocia were included in the three decision tree models, from which the rules for RBM were extracted. The system was equipped with a user-friendly text interface. The percentage of correctly detected easy, moderate and difficult calvings in heifers on the independent test set was 26.13%, 76.52% and 77.27%, respectively. The overall accuracy was 60.12%. The respective values for cows were: 59.18%, 69.01%, 0% and 62.03%. The predictive performance of the constructed system was satisfactory, except for the difficult category in cows.

HydPred: a novel method for the identification of protein hydroxylation sites that reveals new insights into human inherited disease

2016 ◽  
Vol 12 (2) ◽  
pp. 490-498 ◽  
Author(s):  
Shuyan Li ◽  
Jun Lu ◽  
Jiazhong Li ◽  
Ximing Chen ◽  
Xiaojun Yao ◽  
...  
Keyword(s):  
Web Server ◽  
Inherited Disease ◽  
Reliable Tool ◽  
Novel Method ◽  
User Friendly ◽  
Human Inherited Disease

HydPred was presented as the most reliable tool up to now for the identification of protein hydroxylation sites with a user-friendly web server at http://lishuyan.lzu.edu.cn/hydpred/.

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