- New Tool: FASTA Merge May 9, 2020 - Looking for a tool to quickly merge the sequences in pairs of FASTA files? Need to align a set of proteins together? “FASTA merge files pairwise tool” will get the job done. Unlike other commonly used concatenation tools, this tool retains the headers of both FASTA files, by combining them with a divider, which allowsLearn More...
- Tool Spotlight: Update GFF3 from Table May 6, 2020 - Tired of entering notes directly into Apollo? Need to change a gene feature boundary on the fly? Using this tool, those changes and many more are easily accomplished. Quickly and effectively make a large numbers of changes in a short period of time by utilizing this in tandem with the Annotation Table tool. For instance,Learn More...
- Tool upgrade: GFF3 to Genbank May 5, 2020 - This tool is as straightforward as the name implies. Easily convert your GFF3 files to GenBank files by simply inputting the GFF3 annotation file and reference genome FASTA sequence. Galaxy does the rest, outputting a GenBank file that has re-numbered locus tags. Now the tool also adds the translation table qualifier so it is andLearn More...
- Database update: spanins May 2, 2020 - The CPT houses the premier phage spanin protein database, as described by Kongari et al in 2018. We have made a few minor fixes to the entries and converted to the BLAST version 5 database format so as to be compatible with all future BLAST+ suite updates. The updated database is in the locally installedLearn More...
- Tool added: EasyFig April 30, 2020 - EasyFig was recently added to our Galaxy tools to aid in comparing related genomes. Taking GenBank/EMBL files as inputs, users are able to visually compare anywhere from one to dozens of related genomes. As seen below, the mapping allows for rapid identification of variations between the genomes being evaluated. Parameters can be set to adjustLearn More...
- New spanin-finding toolset: ISP, OSP, Find Spanin April 29, 2020 - Didn’t find your spanins in the genome? Want to be sure that you didn’t miss any candidates? Try the new toolset designed just for that purpose. These tools are meant to be used together to help find potential i-spanin/o-spanin pairs. The ISP and OSP candidate tools start with naive gene-calling from an input genomic fasta.Learn More...
- New tool: File Search April 28, 2020 - Looking for a specific term or domain within your analyzed data, like BLAST, InterProScan, or an annotated genome? This tool will scan input files for your desired terms and output the hits for you to peruse. For example, when searching for lysis genes, searching for lysis-related terms within files can be useful. This tool allowsLearn More...
- New tool: Helical wheel April 24, 2020 - Now available in Galaxy is the Helical Wheel tool. This tool allows the user to insert small peptide sequences of alpha helices and visually determine the relative positions of various amino acids with custom coloring. Using this tool is easy; simply insert a peptide sequence of 36 residues or less directly into the input field,Learn More...
- December 2019 Scheduled Downtime December 9, 2019 - Howdy CPT Users! All CPT Services (Website, Galaxy, Galaxy-Pub, and Apollo) will be down for scheduled maintenance Wednesday December 18th, 2019 for several hours starting at 10AM. Some services may be back up intermittently throughout the maintenance window, please refrain from starting any new jobs if you happen to catch it before the announcement thatLearn More...
- CPT Galaxy NCBI BLAST Upgrade November 14, 2019 - Howdy everyone! The Galaxy Admin team is happy to announce that we’ll be upgrading both the BLAST+ tools and databases available on CPT Galaxy. The BLAST tools will be updated to version 2.9.0 and will make several features that the main NCBI site has available for use in Galaxy, such as filtering by Taxonomy IDLearn More...