From a77feefc02be812b27253a35b20b9332a96380ed Mon Sep 17 00:00:00 2001 From: Robert Gifford Date: Sun, 8 Sep 2024 16:49:37 +0100 Subject: [PATCH] Updated web content --- index.html | 339 +-------------------------------- website/html/paleoviruses.html | 2 +- website/html/viruses.html | 2 +- 3 files changed, 3 insertions(+), 340 deletions(-) diff --git a/index.html b/index.html index 0627cc0d..6f1cc9f9 100644 --- a/index.html +++ b/index.html @@ -21,7 +21,7 @@

Resources for comparative genomic analysis of parvov Viruses Paleoviruses - Highlights + Download GitHub @@ -82,343 +82,6 @@

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- Since the emergence of the SARS-COV2 pandemic, many have become familiar with - the use of virus genome data to track the spread and evolution of pathogenic viruses - - e.g. via tools such as NextStrain. - However, it is less widely appreciated that the same kinds of data sets and comparative genomic approaches - can also be used to explore the structural and functional basis of virus adaptations. -

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- The - GLUE software framework - provides an extensible platform for implementing computational genomic - analysis of viruses in an efficient, standardised and reproducible way. - GLUE projects can not only incorporate all of the data items typically used in - comparative genomic analysis - (e.g. sequences, alignments, genome feature annotations) but can also represent the complex - semantic links between these data items via a relational database. - This 'poises' sequences and associated data for application in computational - analysis, minimising the requirement for labour-intensive pre-processing of datasets. -

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- - GLUE projects are equally suited for carrying out exploratory work - (e.g. using virus genome data to investigate structural and functional properties of viruses) - as they are for implementing operational procedures (e.g. producing - standardised reports - in a public or animal health setting). -

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- Hosting of GLUE projects in an online version control system (e.g. GitHub) provides - a mechanism for their stable, collaborative development, as shown below. -

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GitHub hosting figure

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- What is a GLUE project? -

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- GLUE is an open, integrated - software toolkit that provides functionality for storage and interpretation of - sequence data. -

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- GLUE supports the development of “projects” containing the data items - required for comparative genomic analysis - (e.g. sequences, multiple sequence alignments, genome feature annotations, - and other sequence-associated data). -

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Parvovirus GLUE project figure

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- Projects are loaded into the GLUE "engine", creating a relational database - that represents the semantic relationships between data items. - This provides a robust foundation for the implementation of systematic - comparative analyses and the development of sequence-based resources. -

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Using Parvovirus GLUE

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- The core schema of this database can be extended to accommodate - the idiosyncrasies of different projects, and - GLUE provides a scripting layer (based on JavaScript) for developing custom - analysis tools. -

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- Some examples of 'sequence-based resources' built for viruses using GLUE include: - -

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- What does building the Parvovirus-GLUE project offer? -

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- - Parvovirus-GLUE offers a number of advantages for performing comparative sequence - analysis of parvoviruses: - -

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  1. Reproducibility. - For many reasons, bioinformatics analyses are notoriously difficult to reproduce. - The GLUE framework supports the implementation of fully reproducible - comparative genomics through the introduction of data standards and the use - of a relational database to capture the semantic links between data items. -
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  2. Reusable data objects and analysis logic. - For many - if not most - comparative genomic analyses, data preparation is nine - tenths of the battle. The GLUE framework has been designed to ensure that - work spent preparing high-value data items such as multiple sequence alignments - need only be performed once. Hosting of GLUE projects in an online version control - system such as GitHub allows for collaborative management of important data items - and community testing of hypotheses. -
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  3. Validation. - Building GLUE projects entails mapping the semantic links between data items - (e.g. sequences, tabular data, multiple sequence alignments). - This process provides an opportunity - for cross-validation, and thereby enforces a high level of data integrity. -
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  4. Standardisation of the genomic co-ordinate space. GLUE - projects allow all sequences to utilise the coordinate space of a chosen - reference sequence. Contingencies associated with insertions and deletions - (indels) are handled in a systematic way. -
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  5. Predefined, fully annotated reference sequences: - This project includes fully-annotated reference sequences for major lineages - within the Hepadnaviridae family. -
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  6. Alignment trees: - GLUE allows linking of alignments constructed at distinct taxonomic levels - via an ""alignment tree" - data structure. In the alignment tree, each alignment - is constrained to a standard reference sequence, thus all multiple sequence - alignments are linked to one another via a standardised coordinate system. -
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- Building this GLUE project -

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- - On computers with the GLUE software framework - installed, - the Parvovirus-GLUE project can be instantiated by navigating to the project folder, - initiating GLUE, and issuing the following command in the GLUE shell: - - 

-  Mode path: /
-  GLUE> run file buildCoreProject.glue
- - This will build the Parvovirus-GLUE core project by executing the commands in - this file. - -

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- The core project comprises a - dataset designed to represent the phylum in a minimal way (i.e. by including - only one or a handful of annotated reference sequences for each major lineage). -

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- We have also created genus-level, extension projects individual genera within the - subfamily Parvovirinae. - These extensions incorporate a more extensive set of species for this virus family. - Once the core project has been built, the parvoviridae extension project can be - constructed, by executing the commands in - this file, - as follows. - - 

-  Mode path: /
-  GLUE> run file buildGenusLevelProjects.glue
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- Related Publications -

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- - Campbell M, Loncar S, Gifford RJ, Kotin R, and RJ Gifford - (2022) -
- Comparative analysis reveals the long-term co-evolutionary history of parvoviruses and vertebrates. -
- PLoS Biology - [view] -
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- - Hildebrandt E, Penzes J, Gifford RJ, Agbandje-Mckenna M, and R Kotin - (2020) -
- Evolution of dependoparvoviruses across geological timescales – implications for design of AAV-based gene therapy vectors. -
- Virus Evolution - [view] -
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- - Pénzes JJ, de Souza WM, Agbandje-Mckenna M, and RJ Gifford - (2019) -
- An ancient lineage of highly divergent parvoviruses infects both vertebrate and invertebrate hosts. -
- Viruses - [view] -
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- - Callaway HM, Subramanian S, Urbina C, Barnard K, Dick R, Hafentein SL, Gifford RJ, and CR Parrish - (2019) -
- Examination and reconstruction of three ancient endogenous parvovirus capsid proteins in rodent genomes. -
- Journal of Virology - [view] -
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- - Singer JB, Thomson EC, McLauchlan J, Hughes J, and RJ Gifford - (2018) -
- GLUE: A flexible software system for virus sequence data. -
- BMC Bioinformatics - [view] -
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- - Pénzes JJ, Marsile-Medun S, Agbandje-McKenna M, and RJ Gifford - (2018) -
- Endogenous amdoparvovirus-related elements reveal insights into the biology and evolution of vertebrate parvoviruses. -
- Virus Evolution - [view] -
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- - de Souza WM, Tristan TPW, Fumagalli MJ, Araujo J, Sabino-Santos Jr. G, Maia FGM, Acrani GO, Carrasco AOT, Romeiro MF, Modha S, Vieira LC, Ometto TL, Queiroz LH, Durigon EL, Nunes MRT, Figueiredo LTM, and RJ Gifford - (2018) -
- Whole-genome sequencing of parvoviruses from wild and domestic animals in Brazil provides new insights into parvovirus distribution and diversity. -
- Viruses - [view] - -
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- Souza WM, Romeiro MF, Fumagalli MJ, Modha S, de Araujo J, Queiroz LH, Durigon EL, Figueiredo LT, Murcia PR, Gifford RJ. - (2017) -
- Chapparvoviruses occur in at least three vertebrate classes and have a broad biogeographic distribution. -
- J Gen Virol. - [view] - -

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License diff --git a/website/html/paleoviruses.html b/website/html/paleoviruses.html index b6072d87..3093f4bd 100644 --- a/website/html/paleoviruses.html +++ b/website/html/paleoviruses.html @@ -21,7 +21,7 @@

Resources for comparative genomic analysis of parvov Home Viruses - Highlights + Download GitHub diff --git a/website/html/viruses.html b/website/html/viruses.html index 3880a78f..15fd32d9 100644 --- a/website/html/viruses.html +++ b/website/html/viruses.html @@ -23,7 +23,7 @@

Resources for comparative genomic analysis of parvov Home Paleoviruses - Highlights + Download GitHub