Current Protocols in Bioinformatics
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Predicting Genes in Single Genomes with AUGUSTUS
Current Protocols in Bioinformatics - Tập 65 Số 1 - 2019
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 related genomes can be integrated in
order to improve the acc...
Aligning Short Sequencing Reads with Bowtie
Current Protocols in Bioinformatics - Tập 32 Số 1 - 2010
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 Wiley & Sons, Inc.
Using MetaboAnalyst 4.0 for Comprehensive and Integrative Metabolomics Data Analysis
Current Protocols in Bioinformatics - Tập 68 Số 1 - 2019
AbstractMetaboAnalyst (https://www.metaboanalyst.ca) is an easy‐to‐use web‐based
tool suite for comprehensive metabolomic data analysis, interpretation, and
integration with other omics data. Since its first release in 2009,
MetaboAnalyst has evolved significantly to meet the ever‐expanding
bioinformatics demands from the rapidly growing metabolomics community. In
addition to providing a variety o...
Employing ProteoWizard to Convert Raw Mass Spectrometry Data
Current Protocols in Bioinformatics - Tập 46 Số 1 - 2014
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 account. This protocol will aid
researc...
QIIME 2 Enables Comprehensive End‐to‐End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data
Current Protocols in Bioinformatics - Tập 70 Số 1 - 2020
AbstractQIIME 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 platform, to re‐use available
data for ...
Comparative Protein Structure Modeling Using MODELLER
Current Protocols in Bioinformatics - Tập 54 Số 1 - 2016
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 comparative models using
the pro...
Multiple Sequence Alignment Using ClustalW and ClustalX
Current Protocols in Bioinformatics - Tập 00 Số 1 - 2003
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 interpretation of alignments and is
the p...
Using SPAdes De Novo Assembler
Current Protocols in Bioinformatics - Tập 70 Số 1 - 2020
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 Oxford Nanopore).
In this article we p...
Viewing and Editing Assembled Sequences Using Consed
Current Protocols in Bioinformatics - Tập 2 Số 1 - 2003
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 are also given for the use of
Asse...
From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline
Current Protocols in Bioinformatics - Tập 43 Số 1 - 2013
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 methods involved in
variant disco...
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