Current Protocols in Bioinformatics
SCOPUS (SonsInc.)
1934-3396
1934-340X
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Cơ quản chủ quản: John Wiley & Sons Inc.
Lĩnh vực:
Structural BiologyBiochemistryMedicine (miscellaneous)
Các bài báo tiêu biểu
From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices PipelineAbstract This unit describes how to use BWA and the Genome Analysis Toolkit (GATK) to map genome sequencing data to a reference and produce high‐quality variant calls that can be used in downstream analyses. The complete workflow includes the core NGS data‐processing steps that are necessary to make the raw data suitable for analysis by the GATK, as well as the key ... ... hiện toàn bộ
Tập 43 Số 1 - 2013
Comparative Protein Structure Modeling Using MODELLERAbstract Comparative protein structure modeling predicts the three‐dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target‐template alignment, model building, and model evaluation. This unit describes how to calculate... ... hiện toàn bộ
Tập 54 Số 1 - 2016
Multiple Sequence Alignment Using ClustalW and ClustalXAbstract The Clustal programs are widely used for carrying out automatic multiple alignment of nucleotide or amino acid sequences. The most familiar version is ClustalW, which uses a simple text menu system that is portable to more or less all computer systems. ClustalX features a graphical user interface and some powerful graphical utilities for aiding the interpre... ... hiện toàn bộ
Tập 00 Số 1 - 2003
Using MetaboAnalyst 4.0 for Comprehensive and Integrative Metabolomics Data AnalysisAbstract MetaboAnalyst (https://www.metaboanalyst.ca... ... hiện toàn bộ
Tập 68 Số 1 - 2019
Using SPAdes De Novo AssemblerAbstract SPAdes—St. Petersburg genome Assembler—was originally developed for de novo assembly of genome sequencing data produced for cultivated microbial isolates and for single‐cell genomic DNA sequencing. With time, the functionality of SPAdes was extended to enable assembly of IonTorrent data, as well as hybrid assembly from short and long reads (PacBio and Oxfor... ... hiện toàn bộ
Tập 70 Số 1 - 2020
Aligning Short Sequencing Reads with BowtieAbstract This unit shows how to use the Bowtie package to align short sequencing reads, such as those output by second‐generation sequencing instruments. It also includes protocols for building a genome index and calling consensus sequences from Bowtie alignments using SAMtools. Curr. Protoc. Bioinform . 32:11.7.1‐11.7.14. © 2010 by John Wi...
Tập 32 Số 1 - 2010
Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial CommunitiesAbstract QIIME (canonically pronounced “chime”) is a software application that performs microbial community analysis. It is an acronym for Quantitative Insights Into Microbial Ecology, and has been used to analyze and interpret nucleic acid sequence data from fungal, viral, bacterial, and archaeal communities. The following protocols describe how to install QIIME on... ... hiện toàn bộ
Tập 36 Số 1 - 2011
QIIME 2 Enables Comprehensive End‐to‐End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available DataAbstract QIIME 2 is a completely re‐engineered microbiome bioinformatics platform based on the popular QIIME platform, which it has replaced. QIIME 2 facilitates comprehensive and fully reproducible microbiome data science, improving accessibility to diverse users by adding multiple user interfaces. QIIME 2 can be combined with Qiita, an open‐source web‐based platfo... ... hiện toàn bộ
Tập 70 Số 1 - 2020
Employing ProteoWizard to Convert Raw Mass Spectrometry DataAbstract After raw data have been captured by mass spectrometers in biological LC‐MS/MS experiments, they must be converted from vendor‐specific binary files to open‐format files for manipulation by most software. This protocol details the use of ProteoWizard software for this conversion, taking format features, coding options, and vendor particularities into accoun... ... hiện toàn bộ
Tập 46 Số 1 - 2014
Predicting Genes in Single Genomes with AUGUSTUSAbstract AUGUSTUS is a tool for finding protein‐coding genes and their exon‐intron structure in genomic sequences. It does not necessarily require additional experimental input, as it can be applied in so‐called ab initio mode. However, extrinsic evidence from various sources such as transcriptome sequencing or the annotations of closely r... ... hiện toàn bộ
Tập 65 Số 1 - 2019