Swabs to genomes: a comprehensive workflow

The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become almost trivial for research labs with access to standard molecular biology and computational tools. However, there are a wide variety of options available for DNA library preparation and sequencing, and inexperience with bioinformatics can pose a significant barrier to entry for many who may be interested in microbial genomics. The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab) to a published microbial genome; empowering even a lab or classroom with limited resources and bioinformatics experience to perform it.

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Swabs to Genomes: A Comprehensive Workflow

10.7287/peerj.preprints.453v1 ◽

2014 ◽

Cited By ~ 1

Author(s):

Madison I Dunitz ◽

Jenna M Lang ◽

Guillaume Jospin ◽

Aaron E Darling ◽

Jonathan A Eisen ◽

...

Keyword(s):

Molecular Biology ◽

Environmental Sample ◽

Limited Resources ◽

Library Preparation ◽

Computational Tools ◽

Microbial Genomes ◽

Dna Library ◽

Significant Barrier ◽

Barrier To Entry ◽

Standard Molecular Biology

The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become almost trivial for research labs with access to standard molecular biology and computational tools. However, there are a wide variety of options available for DNA library preparation and sequencing, and inexperience with bioinformatics can pose a significant barrier to entry for many who may be interested in microbial genomics. The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab) to a published microbial genome; empowering even a lab or classroom with limited resources and bioinformatics experience to perform it.

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Genome-wide detection and quantitation of RNA distribution by ChIRC13a-seq

10.21203/rs.3.pex-1416/v1 ◽

2021 ◽

Author(s):

Fan Yang ◽

Bogdan Tanasa ◽

Rudi Micheletti ◽

Kenneth A. Ohgi ◽

Aneel K. Aggarwal ◽

...

Keyword(s):

Molecular Biology ◽

Binding Sites ◽

Eukaryotic Genome ◽

Chromatin Binding ◽

Library Preparation ◽

Guide Rnas ◽

Genome Wide ◽

Target Rna ◽

Detailed Protocol ◽

Standard Molecular Biology

Abstract Eukaryotic genome are transcribed extensively, but a majority of transcripts remain functionally uncharacterized. This is most ascribed to lacking of a potent RNA-centric technology that is capable of accurately quantitating putative genomic binding sites for endogenous RNAs. We describe here a detailed protocol for Chromatin Isolation by RNA-Cas13a Complex sequencing (ChIRC13a-seq), based on recently discovered CRISPR-Cas13a from Leptotrichia wadei (LwaCas13a), for profiling of RNA associated chromatin binding cites. ChIRC13a-seq employs biotinylated, enzymatically-dead Cas13a (dCas13a) that is still capable of binding target RNA and guide RNAs (gRNAs) specific for the RNA target of interest to enrich RNA and its chromatin binding sites. This assay can be performed in standard molecular biology laboratories with 2 d taken for ChIRC13a-seq library preparation.

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Biological Nanopores: Engineering on Demand

Life ◽

10.3390/life11010027 ◽

2021 ◽

Vol 11 (1) ◽

pp. 27

Author(s):

Ana Crnković ◽

Marija Srnko ◽

Gregor Anderluh

Keyword(s):

Molecular Biology ◽

Single Molecule ◽

Enzymatic Reactions ◽

Label Free ◽

Natural Sources ◽

On Demand ◽

Label Free Detection ◽

Long Read ◽

Inorganic Molecules ◽

Standard Molecular Biology

Nanopore-based sensing is a powerful technique for the detection of diverse organic and inorganic molecules, long-read sequencing of nucleic acids, and single-molecule analyses of enzymatic reactions. Selected from natural sources, protein-based nanopores enable rapid, label-free detection of analytes. Furthermore, these proteins are easy to produce, form pores with defined sizes, and can be easily manipulated with standard molecular biology techniques. The range of possible analytes can be extended by using externally added adapter molecules. Here, we provide an overview of current nanopore applications with a focus on engineering strategies and solutions.

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Full-UDG treated double-stranded ancient DNA library preparation for Illumina sequencing of ancient dental calculus (reduced input DNA) v1 (protocols.io.bmysk7we)

protocols.io ◽

10.17504/protocols.io.bmysk7we ◽

2020 ◽

Author(s):

Franziska Aron ◽

Christina Warinner ◽

Gunnar U ◽

Guido Brandt

Keyword(s):

Illumina Sequencing ◽

Ancient Dna ◽

Dental Calculus ◽

Library Preparation ◽

Dna Library

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FPGA-Based Accelerators for Bioinformatics Applications

Bioinformatics ◽

10.4018/978-1-4666-3604-0.ch033 ◽

2013 ◽

pp. 605-635

Author(s):

Alba Cristina Magalhaes Alves de Melo ◽

Nahri Moreano

Keyword(s):

Molecular Biology ◽

Research Area ◽

Sequence Profile ◽

Huge Amount ◽

Computational Tools ◽

Computing Power ◽

Open Questions ◽

Similarities And Differences

The recent and astonishing advances in Molecular Biology, which led to the sequencing of an unprecedented number of genomes, including the human, would not have been possible without the help of Bioinformatics. Bioinformatics can be defined as a research area where computational tools and algorithms are developed to help biologists in the task of understanding the organisms. Some Bioinformatics applications, such as pairwise and sequence-profile comparison, require a huge amount of computing power and, therefore, are excellent candidates to run in FPGA platforms. This chapter discusses in detail several recent proposals on FPGA-based accelerators for these two Bioinformatics applications, highlighting the similarities and differences among them. At the end of the chapter, research tendencies and open questions are presented.

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Finishing genomes with limited resources: lessons from an ensemble of microbial genomes

BMC Genomics ◽

10.1186/1471-2164-11-242 ◽

2010 ◽

Vol 11 (1) ◽

pp. 242 ◽

Cited By ~ 38

Author(s):

Niranjan Nagarajan ◽

Christopher Cook ◽

MariaPia Di Bonaventura ◽

Hong Ge ◽

Allen Richards ◽

...

Keyword(s):

Limited Resources ◽

Microbial Genomes

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Genomic DNA Library Preparation for Resistance Gene Enrichment and Sequencing (RenSeq) in Plants

Methods in Molecular Biology - Plant-Pathogen Interactions ◽

10.1007/978-1-62703-986-4_22 ◽

2014 ◽

pp. 291-303 ◽

Cited By ~ 12

Author(s):

Florian Jupe ◽

Xinwei Chen ◽

Walter Verweij ◽

Kamel Witek ◽

Jonathan D. G. Jones ◽

...

Keyword(s):

Resistance Gene ◽

Genomic Dna ◽

Library Preparation ◽

Dna Library ◽

Gene Enrichment ◽

Genomic Dna Library

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Optimization

10.1093/med/9780190667924.003.0003 ◽

2017 ◽

Author(s):

Sanjay Basu

Keyword(s):

Public Health ◽

Diabetes Prevention ◽

Diabetes Prevention Program ◽

Health Department ◽

Pollution Reduction ◽

Limited Resources ◽

Public Health Department ◽

Computational Tools ◽

Reduction Program ◽

Distribution Of Resources

This chapter seeks to determine how can we best allocate limited resources among many different programs. Given a budget to run a program that must be distributed among many different alternative projects (e.g., within a public health department, we might allocate some resources to a vaccination program, another set of resources to a diabetes prevention program, and yet another set of resources to an air pollution reduction program), how can we try to maximize the chances that we allocate limited resources fairly, ensuring that each program has at least the minimal resources that it needs while also ensuring that the distribution of resources maximizes overall public health? This chapter uses computational tools to solve such problems, focusing on how we can make smart decisions to maximize the potential effectiveness or cost-effectiveness of any particular program we’re interested in supporting—a goal known as optimization.

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