Current Protocols in Bioinformatics

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Using MetaboAnalyst 4.0 for Comprehensive and Integrative Metabolomics Data Analysis
Current Protocols in Bioinformatics - Tập 68 Số 1 - 2019
Jasmine Chong, David S. Wishart, Jianguo Xia
AbstractMetaboAnalyst (https://www.metaboanalyst.ca...... hiện toàn bộ
Employing ProteoWizard to Convert Raw Mass Spectrometry Data
Current Protocols in Bioinformatics - Tập 46 Số 1 - 2014
Jerry D. Holman, David L. Tabb, Parag Mallick
AbstractAfter 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
From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline
Current Protocols in Bioinformatics - Tập 43 Số 1 - 2013
Géraldine A. Van der Auwera, Mauricio O. Carneiro, Christopher Hartl, Ryan Poplin, Guillermo del Angel, Ami Levy‐Moonshine, Tadeusz Jordan, Khalid Shakir, David Roazen, Joel Thibault, Eric Banks, Kiran Garimella, David Green, Stacey Gabriel, Mark A. DePristo
AbstractThis 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
Using SPAdes De Novo Assembler
Current Protocols in Bioinformatics - Tập 70 Số 1 - 2020
Andrey D. Prjibelski, Dmitry Antipov, Dmitry Meleshko, Alla Lapidus, Anton Korobeynikov
AbstractSPAdes—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
Predicting Genes in Single Genomes with AUGUSTUS
Current Protocols in Bioinformatics - Tập 65 Số 1 - 2019
Katharina J. Hoff, Mario Stanke
AbstractAUGUSTUS 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
Viewing and Editing Assembled Sequences Using Consed
Current Protocols in Bioinformatics - Tập 2 Số 1 - 2003
David Gordon
AbstractConsed is a program for viewing and editing assemblies prepared by the Phrap assembly program. This unit presents a general introduction to Consed. It also provides instructions for identifying problem regions and searching in Consed. Additional protocols describe creating tags, picking primers, correcting joins and adding and removing reads. Instructions a...... hiện toàn bộ
Aligning Short Sequencing Reads with Bowtie
Current Protocols in Bioinformatics - Tập 32 Số 1 - 2010
Ben Langmead
AbstractThis 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...
Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial Communities
Current Protocols in Bioinformatics - Tập 36 Số 1 - 2011
Justin Kuczynski, Jesse Stombaugh, William A. Walters, Antonio González, J. Gregory Caporaso, Rob Knight
AbstractQIIME (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
Comparative Protein Structure Modeling Using MODELLER
Current Protocols in Bioinformatics - Tập 54 Số 1 - 2016
Benjamin Webb, Andrej Šali
AbstractComparative 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
Multiple Sequence Alignment Using ClustalW and ClustalX
Current Protocols in Bioinformatics - Tập 00 Số 1 - 2003
Julie Thompson, Toby J. Gibson, Desmond G. Higgins
AbstractThe 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
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