- New Tool: 5-column table to Genbank conversion February 16, 2021 - When in the final throes of polishing and proofreading a phage genome’s annotations for submission, you often notice small changes that need to be made. This usually requires back-tracking to an editable file format and can be particularly frustrating when changes get made in a file that cannot be back-converted. Our latest tool is thereLearn More...
- BLAST and InterPro databases updated February 8, 2021 - New year, new rounds of analysis! We just completed our regular updates to BLAST databases from NCBI and UniProt sources, as well as our local curated Canonical phages database. In addition, we updates to the latest InterProScan release. The versions now available on the CPT Galaxy are as listed below. For the nucleotide database: NTLearn More...
- Structural Workflow updated February 8, 2021 - The CPT Galaxy hosts three standard workflows for phage annotation: the Structural and Functional annotation workflows, and the Comparative Genomics Workflow. In preparation for another round of genome annotation with BICH464 students, these workhorses have been polished up and will be released as their first 2021 versions. * Structural Workflow Workflow name: PAP Structural WorkflowLearn More...
- New tool: rho-dependent terminator prediction January 26, 2021 - Stop that transcription! In bacteria, transcription termination can occur by the Rho-independent and Rho-dependent mechanisms. When annotating new phage genomes, the CPT has traditionally focused on identifying likely Rho-independent signals using the TransTermHP tool. Now, we have expanded the ability to look for rho-dependent transcription termination signals in CPT Galaxy with the tool published byLearn More...
- Highlighting community workflows January 21, 2021 - The CPT Galaxy hosts various standard tools and workflows for phage annotation. Below, we highlight a few workflows built and shared among our users for their specific analysis needs. Maybe they will be useful to you as well. * Structural workflow for existing organism Workflow name: Modified PAP Structural Workflow v.2020.06 for updating existing organismPurpose:Learn More...
- New tool: ProphET for prophage prediction January 19, 2021 - Looking for prophages in bacterial genomes? We added the prophage estimation tool ProphET described by Reis-Cunha et al. to CPT Galaxy. The tool uses similarity to a database of prophage genes and calculations of density and boundaries to make its determination. To use ProphET in Galaxy, users need to supply a matched bacterial genome inLearn More...
- New Tool: Collapse Collection converts to single datasets January 8, 2021 - Data stuck in a dataset collection or list when you need it as a single dataset? When you have a history entry in a ‘Collection’, those files can be extracted as single history entries using the Collapse Collections into a single dataset tool. Galaxy was developed as a platform to handle large datasets. The abilityLearn More...
- Tool panel reorganization December 10, 2020 - Does something look different around here? The tool list has been completely reorganized! There are new section headers and groupings to aid in navigating to the exact tool you need, as well as discovering tools you may not have known we have, so do some exploring! Additionally, you will notice a section called ‘Commonly UsedLearn More...
- New Tool: Compare Genbanks December 9, 2020 - Genome annotations are constantly improving. In the process of working on an annotation, or re-annotation, project, you can accumulate various Genbank file versions for the same organism. When you need a wholesale comparison of the number, position/length, and names or notes for each CDS feature, try using our new Compare Genbanks tool. The tool willLearn More...
- Tip: how to extract an SVG file for figure generation December 8, 2020 - Want to publish your Galaxy analyses outputs but hampered by the inability to download high-resolution, editable files of the results for your next manuscript figures? Sometimes we are too and that is what prompted the creation of our latest training material entry under the Additional Analyses section called “How to Extract an SVG file fromLearn More...