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91.1 If you don't already have a sequence conversion tool, download the.91 Building BLAST indices from local sequence files.
89.2 One thing to note in the table above is that uniprot divisions are provided in embl format.89.1 Appendix B – Creating local BLAST databases.88.2 Appendix A – BLAST references and documentation.80.1 (EMBOSS commands exercise continued).80 Exercise – using EMBOSS command line.79.1 If you type the command name followed by -opt then you are prompted for optional.77.1 A comparison of the Jemboss and command line interfaces for EMBOSS programs.77 Biological databases and EMBOSS on Bio-Linux.Imagine you had 100 sequences to blast – you 73.1 You should now see that you have five blastx results files.In this case the list is being generated as the 72.2 The keyword in is followed by a list of things to loop over.72.1 The foreach loop explained step by step.69.1 For the purposes of this tutorial, we will give each BLAST command the explicit location of the BLAST.68 How a BLAST database looks on the file system.67.1 There are many other programs available as part of the BLAST+ release apart from the ones above.64 General considerations for database searching.(This last point has been made easier than ever in the newer BLAST+ programs, where you can, to 56 Converting the shared file to BIOM-format.54 Generating OTU Table and Normalisation.50 Generating Alignment & Distance Matrix.48.1 make_2d_plots.py -i out/bdiv_even146/unweighted_unifrac_pc.txt -o out/bdiv_even146/unweighted_unifrac_2d.41.2 Note: Commands to type are shown in grey boxes like this.41 Examples of running bioinformatics programs on Bio-Linux.
38.1 Naming files and the danger of over-writing previous results.30.1 Common bioinformatics file formats.30 File naming conventions in bioinformatics.29.1 Converting files to different sequence formats used to be a frequent, and often time consuming, task in.28 Often more intuitive and visually pleasing.27 Fast to run once you know the program.25.1 Help Functions within the Programs.25 Part Two: Introduction to Bioinformatics on Bio-Linux.24 Accessing a running program or working with others interactively.21.3.1 Changing permissions on files and directories.