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/.

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 Loss of exon identity is a common mechanism of human inherited disease

2011 ◽  
Vol 21 (10) ◽  
pp. 1563-1571 ◽  
Author(s):  
T. Sterne-Weiler ◽  
J. Howard ◽  
M. Mort ◽  
D. N. Cooper ◽  
J. R. Sanford
Keyword(s):  
Common Mechanism ◽  
Inherited Disease ◽  
Human Inherited Disease

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 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]

In Silico Identification of Protein S-Palmitoylation Sites and Their Involvement in Human Inherited Disease

2015 ◽  
Vol 55 (9) ◽  
pp. 2015-2025 ◽  
Author(s):  
Shuyan Li ◽  
Jiazhong Li ◽  
Lulu Ning ◽  
Shaopeng Wang ◽  
Yuzhen Niu ◽  
...  
Keyword(s):  
In Silico ◽  
Protein S ◽  
Inherited Disease ◽  
In Silico Identification ◽  
Human Inherited Disease
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