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 Lab 3.3

BIO/MIC440: Bioinformatics Lab 3-3

The following sequence is the coding sequence of the HBB (hemoglobin beta) gene in humans.

 

tgtgttcact agcaacctca aacagacacc atggtgcacc tgactcctga ggagaagtct gccgttactg ccctgtgggg caaggtgaac gtggatgaag ttggtggtga ggccctgggc aggctgctgg tggtctaccc ttggacccag aggttccttg agtcctttgg ggatctgtcc actcctgatg ctgttatggg caaccctaag gtgaaggctc atggcaagaa agtgctcggt gcctttagtg atggcctggc tcacctggac aacctcaagg gcacctttgc cacactgagt gagctgcact gtgacaagct gcacgtggat cctgagaact tcaggctcct gggcaacgtg ctggtctgtg tgctggccca tcactttggc aaagaattca ccccaccagt gcaggctgcc tatcagaaag tggtggctgg tgtggctaat gccctggccc acaagtatca ctaagctcgc tttcttgctg tccaatttct attaaaggtt cctttgttcc ctaagtccaa ctactaaact gggggatatt atgaagggcc tt


1.Use this sequence to perform a BLAST search to find the HBB gene from other organisms.

2.Open Biology Workbench and start a session. First, add the human nucleotide coding sequence. IN ALL CASES, BE SURE YOU ARE ADDING THE CODING SEQUENCE! Then find and add the DNA sequences from the chimpanzee, dog, Norway rat, giant panda, domestic yak, crab-eating macaque, and rabbit. FYI: Some genomes may have been sequenced very recently and the gene sequences are "predicted" because they have only been found using programs such as GENSCAN, but no real lab work has been done to verify that those are, in fact, the correct sequences. (However, they probably are).

3.Now that you have eight different DNA coding sequence files, select them all and perform a CLUSTALW analysis, ignoring any warnings that may be given. Import the results of the CLUSTALW analysis and then use DRAWTREE to draw an unrooted phylogenetic tree. Print out the tree.

4.What organism are we most related to based on the HBB gene alignment? Was this expected?

5.Use the DRAWTREE output to describe the relatedness of the eight coding sequences (which sequences are more similar, which are not). Does this make sense with what you know about these eight organisms?

__________________________________________________________________________________

We can make comparisons between certain organisms one gene sequence at a time as we just did. However, sometimes the relatedness of two organisms will differ depending upon which DNA sequence is used for comparison. It is much more powerful to compare entire genomes to each other, and now that the genomes of many organisms have been sequenced, these comparisons are possible. 

We will do a little comparing ourselves by exploring the Human-Mouse Homology Map site. Use the following link to go to the Human-Mouse Homology Map: http://www.ncbi.nlm.nih.gov/projects/homology/maps/

1. How many different chromosomes are there in humans (not counting mitochondrial DNA)?          

In a mouse (not counting mitochondrial DNA)?

2. Go to the mouse X chromosome. Use the "Link to Gene Table View".  Notice that the mouse and human DNA are aligned with respect to where the common genes and markers are located. Of all of the mouse genes on the X chromosome, how many can be placed definitively on human chromosomes other than the X?

3.Using the mouse chromosomes as the "reference", examine syntenic blocks between mouse and human on chromosome 7. How well do the X chromosomes overlap in these two organisms compared to the chromosome 7 overlap in these two organisms?

 List the five human chromosomes that share major syntenic blocks with mouse chromosome 7.

4. Now go to the human X chromosome. What human gene is found at human position 31,047,266 (in bp)?

Click on the human gene at this location to go to Entrez Gene. What is the name of the protein encoded by this gene?

With what disease is the gene associated?

How large is this gene in humans? How does the size of this gene compare to the size of other human genes?

 

5. Obtain the coding sequence (about 11,000 kb), and paste it into Biology Workbench. Do the same thing for the mouse version of the DMD coding sequence. Then align the two coding sequences in Workbench using BL2SEQ (i.e., BLAST two sequences). DO NOT PRINT THIS ALIGNMENT OR I WILL FAIL YOU IN THIS COURSE!!!!! 

Interpret the results of this alignment in terms of the percent DNA sequence identity and the number of gaps. Is there a good match between the human and mouse DMD genes?

 

Given the identity between the two between the two DMD coding sequences and the respective locations of the DMD genes in each organism, what does this suggest about the comparative function of the Dmd proteins in each organism? What phenotype would you expect in a mouse that has a mutation in this gene?  

 

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