TaxaBLAST Search

Uploading sequence data

• On the main TaxaBLAST page, click on the “select file(s)” button to select one or more FASTA files to upload. 
  • Note: On an iPhone or iPad, you can only select “.txt” files, so any FASTA files you want to upload need to be renamed first. For example, “myFastaFile.fasta” should be renamed to “myFastaFile.txt”.
• For now, TaxaBLAST only supports FASTA files containing nucleotide sequences, but we plan to also support protein sequences in the near future.
• You can upload up to 100 sequences at a time. The sequences can be in a single file or multiple files as long as the total file size is less than 1GB.
• To return to the file selection page for a new TaxaBLAST search, navigate to TaxaBLAST using the ICTV menu. Also, many TaxaBLAST pages include a green button labeled “New search”. Clicking on this button will open the file selection page in a new browser tab. 

Jobs

• Behind the scenes, your data and results are grouped together as a “job” with a unique identifier (the “job UID”), a name, and other information about the submission and results.
• After your TaxaBLAST job has been successfully submitted, the page's URL will be updated to include your job's unique identifier (UID). You can paste this URL into any browser to view the job's results at a later date.
• Please note that job results are automatically deleted 1 month after submission, so please save copies of your result data on your local machine!
• If you experience an error with TaxaBLAST, please email your sequences (and if possible, the job UID) to info@ictv.global.

Job submission

• After your files have been selected, you can provide a custom name for the job, or a default name will be created by TaxaBLAST after submission.
• After confirming that the list of filenames to upload is correct, click on the “submit”(?) button to upload them to TaxaBLAST and begin processing.
• Depending on the number and size of the sequences that are uploaded, your TaxaBLAST results may not be immediately available. 
• If your job's results do not appear within 5-10 seconds, we recommend copying the page's URL so you can return later to view your results. For convenience, you can click on the “copy” button to copy the page's URL to your clipboard so it can be pasted into a document for later reference.

Interpreting your results

• Job details
  • The job details include the job's name, submission date, its status, the amount of time it took to complete, and information about the versions of TaxaBLAST and the BLAST database that were used for processing. (TODO: maybe list and define each job details field?)
• File(s)
  • TaxaBLAST results are grouped by 1) uploaded file(s) and 2) the FASTA sequences included in a particular file. 
  • Clicking on the arrow/chevron to the left of the file name (or anywhere in the tile containing the filename) will display a row of data for every sequence contained in the uploaded file, each of which corresponds to a BLAST query.
• Sequences
  • Each sequence row includes the BLAST query ID,the number of BLAST hits, and several buttons that provide different ways to view sequence-specific TaxaBLAST results:
  • “View BLAST hits”: Display detailed TaxaBLAST results for the sequence/query in a new browser tab. This includes ranked ICTV taxa, each with a table of scored High-scoring Segment Pairs (HSPs) that were used to associate the ICTV taxon with the FASTA sequence. 
  • “View alignments”: Open a page with the standard results generated by BLAST in a new browser tab.
  • “Download results as CSV”: Download a concise summary of the sequence’s TaxaBLAST results, c formatted as a comma-separated- value (CSV) file that can be viewed as a spreadsheet.