To day we will work at your own pace and perform the following sequence of steps.
1. Go to the NCBI web site and download the complete Mycoplasma Genitalium G37 genome from the Nucleotide database. This bacteria is the smallest known genome that can constitute a cell although there are others that are smaller which are parasitic. Its Accession number is L43967.2
2. Change its name to mycogen.gl.
3. To begin your program open Notepad++ write some Perl code that will read the file and write out the file to both the file mycogenout.txt and to the screen. Include the die option in the open command for the myco file. This program after it is working will your starting point and subsequently modified to handle the following requirements.
4. Modify the abouve program so that it will print out the lines in the file that start with a gene in the source column. Check that the output is what you want and does not include other lines.
5. Now drop the print line (or comment it out) and just calculate the number of genes that we just printed. Print it with comment.
6. Include additional code to print out the percent of these genes that are complementary genes.
7. Now add code to count the number of tRNA sequences that occur as well as the percent of these that are complementary.
8. Now at bottom of your program close the input file and reopeen it . Now add code underneath this new open that prints out the first 10 lines that occur AFTER the work ORIGIN. Print these lines without the numbers in front and the spaces between the sections.
- NOTES: If you are interested check out mycoplasma laboratorium. This is a new species created from parts of genitalium by Craig Venter and others.