annotation

Explore MetaPathPredict and OMEGGA: Tools for Bioinformatics

Tonight I watched another KBase Science Session: Data integration to support (or refute) predictions. “Integrating data to predict functions for gaps in metabolic models” was the title of Bill Nelson’s session. Nelson is from the Pacific Northwest National Laboratory. The work was part of two PNNL SFA projects: a soil microbiome project and a persistence […]
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Understanding DRAM and Genome Analysis at ISME19

I continue watching the ISME19 KBase workshop: “From Reads to Function, Day 2.” Jared Ellenbogen presented next. They spoke about “DRAM and genome-resolved inference.” Ellenbogen spoke about analyzing the fifteen genomes studied during the workshop with DRAM. The outputs of DRAM were described: a heat map with every row corresponding to a different genome or […]
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Understanding the NO-MISS Workflow for Microbial Sequencing

Tonight, I watched the second half of a new Knowledge Exchange session focusing on “Sequencing and analysis of nanopore-only microbial isolates with the NO-MISS workflow.” Different extraction methods produced varying yields. Bead-beating and enzymatic lysis extractions affect read length and throughput, while fungal samples produce lower yields. Some potential issues include incomplete lysis and contaminants. Additional clean-up […]
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Insights into Medicinal Plant Metabolites

I am preparing to go to Seattle tomorrow to visit the Allen Institute again! Tonight I watched Ronja Friedhoff from the Technische Universitat Braunschweig in Germany present at London Calling 2024. The title of the session is “Accessing the biosynthetic gene repertoire of medicinal plants.” Friedhoff started by asking, “What secrets are hidden in plant […]
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A Useful Genome Assembly Report

John Davey from the University of York in the UK presented at London Calling 2019 on “Tapestry: assessing small eukaryotic genome assemblies with long reads.” Davey spoke about the tool and mentioned they are a Nanopore Service Certified core. Davey spoke about Galdieria sulphuraria with a genome of 10-20 Mb with several chromosomes. This organism […]
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Identifying Full-length Transcripts through Innovative Capture Techniques

As part of the 2019 London Calling lightning talks, Silvia Carbonell Sala from the Centre for Genomic Regulation in Spain presented on “CapTrap-CLS: full-length RNA capture long-seq for GENCODE.” They explained how our genomes encode long non-coding RNAs. Their functions, however, may not be known. Carbonell Sala is part of the GENCODE lncRNA Capture Project […]
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Liftoff and Novel Gene Annotation

Alaina Shumate from Johns Hopkins University was a speaker at the Nanopore Community Meeting 2021. Shumate was a graduate student and worked on “The annotation of novel genes in a complete human genome.” They noted that in 2003, scientists “finished” the human genome, but reions were still incomplete. In 2021, the Telomere-to-Telomere (T2T) Consortium was […]
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Assembly of A Model of Plant Evolution

Issa Diop from the University of Zurich in Switzerland presented at London Calling 2021 on “Chromosomal-scale assembly of the liverwort Marchantia paleacea.” Diop discussed chloroplasts and endosymbionts before introducing Marchantia as a model of plant evolution. Marchantia has a haploid-dominant life cycle with a genome size of 280 Mbp. There are eight autosomes and 1 […]
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A Guide to Structural Variation Analysis

Today I watched the Knowledge Exchange session from Nanopore Learning about “A beginner’s guide to structural variation analysis: from discovery to basic annotation.” Steven Rudd, a bioinformatics expert at Oxford Nanopore Technologies, shared a couple of slides and then explored the structural variation tutorial. A structural variant (SV), Rudd said, is typically considered as “a […]
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