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Using the MINT Database to Search Protein Interactions.
This article provides protocols for searching MINT over the Internet, using the new MINT Web Page. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Searching MINT over the internet Alternate Protocol: MINT visualizer Basic Protocol 2: Submitting interaction data. PMID: 31945268 [PubMed - in process] (Source: Current Protocols in Bioinformatics)
Source: Current Protocols in Bioinformatics - January 18, 2020 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

How to Illuminate the Druggable Genome Using Pharos.
Authors: Sheils T, Mathias SL, Siramshetty VB, Bocci G, Bologa CG, Yang JJ, Waller A, Southall N, Nguyen DT, Oprea TI Abstract Pharos is an integrated web-based informatics platform for the analysis of data aggregated by the Illuminating the Druggable Genome (IDG) Knowledge Management Center, an NIH Common Fund initiative. The current version of Pharos (as of October 2019) spans 20,244 proteins in the human proteome, 19,880 disease and phenotype associations, and 226,829 ChEMBL compounds. This resource not only collates and analyzes data from over 60 high-quality resources to generate these types, but also...
Source: Current Protocols in Bioinformatics - January 5, 2020 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

NCBI's Conserved Domain Database and Tools for Protein Domain Analysis.
Authors: Yang M, Derbyshire MK, Yamashita RA, Marchler-Bauer A Abstract The Conserved Domain Database (CDD) is a freely available resource for the annotation of sequences with the locations of conserved protein domain footprints, as well as functional sites and motifs inferred from these footprints. It includes protein domain and protein family models curated in house by CDD staff, as well as imported from a variety of other sources. The latest CDD release (v3.17, April 2019) contains more than 57,000 domain models, of which almost 15,000 were curated by CDD staff. The CDD curation effort increases coverag...
Source: Current Protocols in Bioinformatics - December 20, 2019 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

The MathIOmica Toolbox: General Analysis Utilities for Dynamic Omics Datasets.
Authors: Mias GI, Zheng M Abstract MathIOmica is a package for bioinformatics, written in the Wolfram language, that provides multiple utilities to facilitate the analysis of longitudinal data generated from omics experiments, including transcriptomics, proteomics, and metabolomics data, as well as any generalized time series. MathIOmica uses Mathematica's notebook interface, wherein users can import longitudinal datasets, carry out quality control and normalization, generate time series, and classify temporal trends. MathIOmica provides spectral methods based on periodograms and autocorrelations for auto...
Source: Current Protocols in Bioinformatics - December 20, 2019 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

The ENCODE Portal as an Epigenomics Resource.
Authors: Jou J, Gabdank I, Luo Y, Lin K, Sud P, Myers Z, Hilton JA, Kagda MS, Lam B, O'Neill E, Adenekan P, Graham K, Baymuradov UK, R Miyasato S, Strattan JS, Jolanki O, Lee JW, Litton C, Y Tanaka F, Hitz BC, Cherry JM Abstract The Encyclopedia of DNA Elements (ENCODE) web portal hosts genomic data generated by the ENCODE Consortium, Genomics of Gene Regulation, The NIH Roadmap Epigenomics Consortium, and the modENCODE and modERN projects. The goal of the ENCODE project is to build a comprehensive map of the functional elements of the human and mouse genomes. Currently, the portal database stores over 500...
Source: Current Protocols in Bioinformatics - November 23, 2019 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Using INTERSPIA to Explore the Dynamics of Protein-Protein Interactions Among Multiple Species.
This article contains a basic protocol describing how to visualize diverse patterns of PPIs of input proteins in multiple species, and how to use them for functional analysis in the web interface. INTERSPIA is freely available at http://bioinfo.konkuk.ac.kr/INTERSPIA/. © 2019 by John Wiley & Sons, Inc. Basic Protocol: Running INTERSPIA using a list of input proteins. PMID: 31751498 [PubMed - in process] (Source: Current Protocols in Bioinformatics)
Source: Current Protocols in Bioinformatics - November 23, 2019 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Population Genetic Inference With MIGRATE.
Authors: Beerli P, Mashayekhi S, Sadeghi M, Khodaei M, Shaw K Abstract Many evolutionary biologists collect genetic data from natural populations and then need to investigate the relationship among these populations to compare different biogeographic hypotheses. MIGRATE, a useful tool for exploring relationships between populations and comparing hypotheses, has existed since 1998. Throughout the years, it has steadily improved in both the quality of algorithms used and in the efficiency of carrying out those calculations, thus allowing for a larger number of loci to be evaluated. This efficiency has been e...
Source: Current Protocols in Bioinformatics - November 23, 2019 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Using MetaboAnalyst 4.0 for Comprehensive and Integrative Metabolomics Data Analysis.
This article provides an overview of the main functional modules and the general workflow of MetaboAnalyst 4.0, followed by 12 detailed protocols: © 2019 by John Wiley & Sons, Inc. Basic Protocol 1: Data uploading, processing, and normalization Basic Protocol 2: Identification of significant variables Basic Protocol 3: Multivariate exploratory data analysis Basic Protocol 4: Functional interpretation of metabolomic data Basic Protocol 5: Biomarker analysis based on receiver operating characteristic (ROC) curves Basic Protocol 6: Time-series and two-factor data analysis Basic Protocol 7: Sample size estimation and powe...
Source: Current Protocols in Bioinformatics - November 23, 2019 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Community Curation and Expert Curation of Human Long Noncoding RNAs with LncRNAWiki and LncBook.
Authors: Ma L, Cao J, Liu L, Li Z, Shireen H, Pervaiz N, Batool F, Raza RZ, Zou D, Bao Y, Abbasi AA, Zhang Z Abstract In recent years, the number of human long noncoding RNAs (lncRNAs) that have been identified has increased exponentially. However, these lncRNAs are poorly annotated compared to protein-coding genes, posing great challenges for a better understanding of their functional significance and elucidating their complex functioning molecular mechanisms. Here we employ both community and expert curation to yield a comprehensive collection of human lncRNAs and their annotations. Specifically, LncRNAW...
Source: Current Protocols in Bioinformatics - September 17, 2019 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Ploidy- and Purity-Adjusted Allele-Specific DNA Analysis Using CLONETv2.
Authors: Prandi D, Demichelis F Abstract High-throughput DNA sequencing technology provides base-level and statistically rich information about the genomic content of a sample. In the contexts of cancer research and precision oncology, thousands of genomes from paired tumor and matched normal samples are profiled and processed to determine somatic copy-number changes and single-nucleotide variations. Higher-order informative analyses, in the form of allele-specific copy-number assessments or subclonality quantification, require reliable estimates of tumor DNA ploidy and tumor cellularity. CLONETv2 provides...
Source: Current Protocols in Bioinformatics - September 17, 2019 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Using MARRVEL v1.2 for Bioinformatics Analysis of Human Genes and Variant Pathogenicity.
Authors: Wang J, Mao D, Fazal F, Kim SY, Yamamoto S, Bellen H, Liu Z Abstract One of the greatest challenges in the bioinformatic analysis of human sequencing data is identifying which variants are pathogenic. Numerous databases and tools have been generated to address this difficulty. However, these many useful data and tools are broadly dispersed, requiring users to search for their variants of interest through human genetic databases, variant function prediction tools, and model organism databases. To solve this problem, we collected data and observed workflows of human geneticists, clinicians, and mode...
Source: Current Protocols in Bioinformatics - September 17, 2019 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Predicting Sequence Features, Function, and Structure of Proteins Using MESSA.
This article reveals how to access MESSA via the Web and shows how to input a protein sequence to analyze using the MESSA web server. It also includes a detailed explanation of the output from MESSA to aid in better interpretation of results. © 2019 by John Wiley & Sons, Inc. PMID: 31524991 [PubMed - in process] (Source: Current Protocols in Bioinformatics)
Source: Current Protocols in Bioinformatics - September 17, 2019 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Using Mothur to Determine Bacterial Community Composition and Structure in 16S Ribosomal RNA Datasets.
Authors: Chappidi S, Villa EC, Cantarel BL Abstract The 16S ribosomal RNA (rRNA) gene is one of the scaffolding molecules of the prokaryotic ribosome. Because this gene is slow to evolve and has very well conserved regions, this gene is used to reconstruct phylogenies in prokaryotes. Universal primers can be used to amplify the gene in prokaryotes including bacteria and archaea. To determine the microbial composition in microbial communities using high-throughput short-read sequencing techniques, primers are designed to span two or three of the nine variable regions of the gene. Mothur, developed in 2009, ...
Source: Current Protocols in Bioinformatics - September 17, 2019 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

R Tutorial: Detection of Differentially Interacting Chromatin Regions From Multiple Hi-C Datasets.
We describe the process of obtaining Hi-C data from public repositories and give suggestions for pre-processing pipelines for users who intend to analyze their own raw data. We then describe the data normalization and comparative analysis process. We present three protocols describing the use of the multiHiCcompare, diffHic, and FIND R packages, respectively, to perform a comparative analysis of Hi-C experiments. Finally, visualization of the results and downstream interpretation of the differentially interacting regions are discussed. The bulk of this tutorial uses the R programming environment, and the processes describe...
Source: Current Protocols in Bioinformatics - May 29, 2019 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Using PconsC4 and PconsFold2 to Predict Protein Structure.
Authors: Bassot C, Menendez Hurtado D, Elofsson A Abstract In spite of the fact that there has been a significant increase in the number of solved protein structures, structural information is missing for many proteins. Although structural information is codified in the amino acid sequence, computational prediction using only this information is still an unsolved problem. However, one successful method to model a protein's structure starting from the primary sequence is to use contact prediction derived from multiple sequence alignment (MSA). Here we use our contact predictor PconsC4 to generate a list of ...
Source: Current Protocols in Bioinformatics - May 9, 2019 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research