Command Line Examples

Command Line Examples

New Blast2GO Command Line Examples

(Version 1.4 release date: 01/10/2015)

In the Blast2GO Command Line Manual (PDF) you can now find several practical examples which will help you to get started with Blast2GO over the command line.

Here is a quick list of these examples:

  • Load a DNA fasta file, add the corresponding blast results and perform GO mapping and functional annotation. Furthermore, we want to save the .dat file and the PDF report at the current directory with a given name.
  • Load nucleotide sequences, run local blast against SwissProt database, mapping and annotation. Save the 3 combined graphs in a folder with nameprefix localblastSwissprot in .svg, .b2g and .txt format. In this example, a blast, mapping and annotation statistics will also be stored. Finally, the whole project will be saved in the example_data folder in .b2g format and also the corresponding log file.
  • Load nucleotide sequences, load the new version (.json or .xml2) of blast results from a zip file, run mapping and annotation. Save the whole project and its report as example_json.b2g.
  • Load a .b2g file from a given folder, which does not contain InterProScan and run it using IPS parameter. This example will save the InterProScan results in a folder as well as the whole project including them.
  • Convert sequences to protein and save as fasta file.
  • Load a .b2g file from the given folder, which does not contain InterProScan and run it using ips parameter.
  • Generate Combined Graphs locally without an internet connection.
  • Load a protein fasta file, add the corresponding blast results and execute mapping and annotation. All files will be saved with the nameprefix and in a provided workspace folder with additional statistics charts.
  • Load a .dat file, apply plants GO Slim and save the results as .b2g, which will be saved with the default nameprefix and at the current directory.
  • Load a fasta file, a blast result file and InterProScan 5.0 files, perform mapping, annotation and ANNEX. Then create all 3 GO graphs and all statistical charts. As a result, we will obtain the .b2g and the PDF report, which will be saved with the default nameprefix in the current directory.
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Blast2GO is now part of OmicsBox