This project entails utilization of the Gene Inspector software to analyze a large file of DNA sequence. The report for the project will be a Gene Inspector "Notebook" file submitted on a floppy disk. Your Notebook file must start with a table of contents, and each item should be "bookmarked" for easy display/viewing.
Hopefully you have been through the 10 tutorials in the Mini-Manuals given to each of you. Play particular attention to Tutorial #1 on the Notebook. You will need to know what text objects, aliases and bookmarks are and how to create them. Learn also how to create an appendix to your notebook.
Many of the features used in the Notebook are accessed through the "Notebook" menu. Be sure to check out the Notebook -> Tool Extensions as well as Notebook -> Tools. Here you will find some of the features in common computer drawing programs that can be used in the Notebook mode.
Get your sequence file from the Jhana/MOLB 550.Seqs directory (login instructions from class notes). Open the file by double clicking and you will be in "Sequence editor" mode.
Under New Analysis, perform Open Reading Frame, TestCode and CodonPreference analyses on your sequence. All sequences are Bacillus subtilis sequences and you should select the codon bias for that organism in the Analysis setup dialog boxes (see pictures below).
Using the information in Tutorial 7, create a Notebook entry containing your formated sequence with translations of only the most likely open reading frames longer that 90 amino acids and restriction sites for all commercially available 6 base cutters.
Save the result of all analyses in your notebook, with appropriate annotation
and bookmarks. You may want to put some information in appendices at your
discretion. Back up your work on a floppy!