[New Workshop] Bioc2022 Draft Lakshman

[ahl27]

Please supply the following information:

Short title: Comparative Genomics with DECIPHER and SynExtend Workshop URL: https://github.com/ahl27/CompGenomicsBioc2022 Workshop docker image: ghcr.io/ahl27/compgenomicsbioc2022:latest Workshop port: 8787 Workshop memory request: 4GB Workshop description:

In the past decade, the number of sequenced proteins with unknown functions has grown exponentially, while the number of experimentally analyzed proteins has increased at a relatively constant rate. To assign functions to more proteins, many in silico methods have been produced to predict protein function purely from gene sequence data. These methods rely on a ‘guilt-by-association’ analysis to detect genes that are likely involved in common functional pathways.

We have developed two Bioconductor packages with many functions for comparative genomics. This workshop will highlight a broad spectrum of tools for comparative genomics through the lens of a specific application: predicting the functional association between proteins to formulate hypotheses about the unknown role of new proteins. Along the way, we will cover several topics:

• Finding and importing genomes into a sequence database with the DECIPHER package
• Gene calling and annotation using the DECIPHER package
• Identification of clusters of orthologous genes using the SynExtend package
• Construction of alignments and phylogenetic trees using the new TreeLine function in the DECIPHER package
• Prediction of functional associations using ProtWeaver in the SynExtend package

This talk will specifically focus on new features to DECIPHER and SynExtend: TreeLine() for phylogenetic reconstruction, and ProtWeaver for guilt-by-association analysis. All examples will be performed on a real dataset of Mycoplasma genomes.

At the conclusion of this workshop, participants will have gained expertise in a wide variety of tools for bioinformatic analyses, including sequence alignment, phylogenetic reconstruction, ortholog detection, functional annotation, and detection/quantification of selective pressure. These packages are optimized for application at scale, allowing users to conduct analyses on large datasets.

Add any additional notes below.

Webpage is located at https://www.ahl27.com/CompGenomicsBioc2022/articles/CompGenomicsBioc2022.html. Sections are broken into individual pages because I thought this was a cleaner flow than one super long Rmd page. Each page highlights the topics that will be covered for that section; full tutorials will be written prior to the June 17 deadline.

2GB of RAM should be sufficient, but this may change when I finish and test the tutorials.

A Setup page is included to future proof the tutorial so it can be accessed outside of the workshop timeframe--this page will be skipped during the workshop itself.

[seandavi]

Thanks, @ahl27. Your workshop has been added to Orchestra.

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