Speaker: Petr Novák from Biology Centre of the Czech Academy of SciencesRepeatExplorer Galaxy Server provides several tools for discovering and annotation of repetitive elements. Most notably, these include tools such as RepeatExplorer2 or TAREAN pipelines, which can be used to characterize repetitive sequences directly from unassembled sequence reads. Several other tools on the RE server can be also used to annotate repeats in genome assemblies.One of these tools that is suitable for annotation of assemblies is the tool DANTE. DANTE annotate and classifies transposable elements based on the similarities of their sequences to conserved protein domains in the REXdb database. Because REXdbs lineage-based classification system is universally applicable to elements from phylogenetically distant taxa, it also allows comparative studies of LTR -retrotransposon composition across a wide range of species. In addition, application of DANTE to assembled genomic sequences can improve annotation of repetitive DNA and reveal lineage-specific distribution patterns of LTR -retrotransposons along assembled chromosomes.The second tool that can be used for whole genome assembly annotation is the “Repeat Annotation Pipeline”. This tool uses the results of the RepeatExplorer2 pipeline as the basis for creating a species-specific library of repetitive sequences. This library can be further manually curated and then used to annotate whole genome assemblies. Comparison of genome annotation based on the Repeat Annotation Pipeline and annotation based on RepeatExplorer2 from unassembled reads can be used as an indirect criterion for completeness of genome assemblies.The results of DANTE and the Repeat Annotation Pipeline can be visualized directly on the RepeaExplorer Galaxy Server using the Jbrowse genomic browser. All tools are available on https://repeatexplorer-elixir.cerit-sc.cz/Registration is not needed.Join the webinar in GoToMeeting»We value your opinion. Please give us your feedback on the webinar»Practical examples of how to use the discussed RepeatExplorer tools on the Galaxy server will be presented in a subsequent Genome annotation & Galaxy Large Data Handling online workshop» on November 4, 2021, from 2:00 pm to 4:00 pm.Note: the webinar will be recorded and the recording will be used on the ELIXIR CZ website, social media, in ELIXIR CZ e-publications, or in any other ELIXIR CZ online materials.
This workshop is open to everybody interested in Galaxy and consists of two main parts:The first part of the workshop (starting at 14:00) will be hands-on and introduce attendees to some advanced Galaxy’s capabilities. Namely we will walk through the best
projít na článekNucleic Acid Conformations (dnatco.datmos.org)Jiří Černý from BTUA detailed description of the dnatco.datmos.org web server implementing the universal structural alphabet of nucleic acids will be presented. The web server performs an assignment of the nuc
projít na článekELIXIR and Galaxy ProjectMartin Čech from IOCBGalaxy is a tool that assists scientists with making their software pipelines reproducible, portable, and easy to share. This session presents a 10,000 feet overview of the Galaxy Project what it is, what it
projít na článekAfter the summer break, the series of webinars introducing our services is back. Learn about tools and databases developed by ELIXIR CZ, which have great potential to help you in your daily research work. Every Friday at 9:30am, you can have a closer look
projít na článekA course is being organized in Prague, hosted by the Czech ELIXIR Node lead institute in cooperation with the nodes involved in ELIXIR-EXCELERATE task 10.3 “Capacity Building in Genome Assembly and Annotation”. Some of the most experienced assembly and an
projít na článek