- CPT Galaxy-Apollo update (Oct 27, 2021) October 27, 2021 - Howdy, We are beginning to restore all of our services as long awaited. As always, we thank you for your continued patience and support. We are currently in the process of replacing our file server. We encourage users to limit their use of the system for the time being and download any data they wouldLearn More...
- CPT Galaxy-Apollo update (Oct 20, 2021) October 20, 2021 - Howdy! The CPT Galaxy-Apollo system is currently undergoing maintenance due to multiple simultaneous hardware failures that affected our file server. The file server has now been moderately stabilized and we are continuing to migrate our system to new hardware. Thank you for your patience, and hopefully the rest of our services will be returning soon.Learn More...
- Structural Workflow & ShineFind updates March 11, 2021 - A new version of the Structural annotation workflow has been released! The v2021.02 workflow has an updated ShineFind tool, which searches upstream of the start codon of an open reading frame for Shine-Dalgarno sequences. * Structural Workflow: PAP Structural Workflow v2021.02 Notable updates: latest version of the ShineFind tool improves selection of spacing between theLearn More...
- Functional Workflow updated March 5, 2021 - The Functional workflow has now been released as its first 2021 version. Notable updates for the PAP Functional Workflow v2021.01 include: evidence tracks rearranged and labelled with more intuitive groupings new signal outputs: LipoP and SignalP Note: Since last year, this NR BLASTp job is restricted to phage only to speed up the analysis. BLASTpLearn More...
- 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...