Bioinformatics II – FYN
Part 1. Publically Available Genomes.
1) How many primate genomes are represented on the browser?
2) What human assemblies are available on the browser? What is the most current human genome assembly?
3) What primate(s) that are available to browse are most distantly related to human?
4) How many drosophila genomes are represented on the browser?
5) What non-eukaryotic organism(s) is(are) represented? What is the assembly date for this(these) organism(s)?
Part 2. Using the Genome Browser.
1) What is the size of the current display?
2) Hovering over various parts of the longest isoform for MTOR, how many exons does this isoform of the gene have?
3) Based on the information on this summary page, what is the description for this gene and what gene family does it belong to?
4) How many tracks are still displaying information and which tracks are these?
5) What is the most likely explanation for this sequence being present in human, chimp, gorilla, and gibbon, but not the other organisms?
6) Chromosome 1 is the longest human chromosome. In bases, what is the length of chromosome 1?
7) How long is chromosome 21? How many times longer is chromosome 1 than chromosome 21?
8) How long is this sequence?
9) What is the length of the mRNA sequence? What accounts for the difference in length between the mRNA sequence and the coding sequence you identified in the previous question?
10) How many tissues are represented in the figure?
11) Which tissue is reported to have the highest amounts of expression? Does this make sense for this gene, why or why not?
Part 3. Tools: BLAT
1) What is the percent identity between the human query sequence and the top chimp hit? What is the corresponding score? Where in the chimp genome is their homolog of TMEM99 found?
2) How many differences are there between the human sequence and the chimp sequence?
3) What is the score and percent identity for each of these organisms? Make sure to investigate the details link. Based on your interpretation of the BLAT results and the corresponding alignments, is TMEM99 present in gorilla, rhesus, mouse, elephant, and chicken?
Make a table to summarize your answers for this section of questions.
Part 4. Exploring the Drosophila genome assemblies.
1) What chromosome in D. melanogaster is the vestigial (vg) gene located on? What are the coordinates for the gene?
2) In a previous lab, you should have found the vestigial and brown body (bw) gene of drosophila to be some centimorgans apart. In bases, how far apart are these two genes?
3) Manipulate the navigation controls or position/search term box so that it shows both the vg and bw genes in the same display (If gene names are not listed in the display, then click on the block of transcripts immediately under the “RefSeq gene predictions from NCBI” This will alter the display density.). Take a screen shot of this display and highlight the location of the vg and bw genes.