Do you love protein structures? There are many interesting standardized file formats that are used in structural biology. Explore some of these datasets:
When you're starting a collection of bibliographic material, it can sometimes be useful to download bibliographic information in bulk from pubmed. Try the following exercise that will create a timeline of publication dates for a given researcher:
Bed files are very common standardized file formats. They are fairly compact ways of representing locations on a genome. For this exercise, see if you can upload your .bed file to a genome browser. A genome browser is an interface that can allow you to cruise around the genome. You can zoom out and see everything on a chromosome, or zoom into a specific gene or location. There are two main genome browsers: IGV which is a local program you can install. Or UCSC Genome browser, which is an online resource.
The sacCer3_tRNA.bed file you made contains the locations of all the tRNA gene in the yeast genome. Let's try to upload this file to the UCSC Genome browser. See if you can follow along with these commands:
sacCer3_tRNA.bedby selecting CHOOSE FILE and then pushing SUBMIT after you have directed to your .bed file.
Do you remember all the steps you took in Assignment 2 to extract out a .bed file containing the tRNA loci from a large, annotated .gff file with fasta info at the end? Can you make a very simple .sh script that makes a .bed file containing the loci for all the introns in the yeast genome? How many spliced genes are there? It's not many!
There is a wealth of biological data out there. Find a biological database relevant to your field of study and download some datasets. What are the common file types? Which can be read as text files?
Do you order a lot of oligos? If so, the companies typically e-mail you in standardized formats. Try downloading all the e-mails and pulling out relevant information about each oligo based on their standardized format. You can then save these to an .xls sheet or a database program. Your database might be quite basic after Week2 of the course, but after Week4, it may become more sophisticated. If you are interested in making more apps like this, consider taking the python course.