Lab 5 - Paul Gonzales BIO 206L Session: 49540 Lab 5 1) Use...

Info iconThis preview shows pages 1–2. Sign up to view the full content.

View Full Document Right Arrow Icon
Paul Gonzales BIO 206L Session: 49540 Lab 5 1) Use of the BLAST (Basic Local Alignment Search Tool) was used to search for protein sequences and nucleotide sequences of various organisms. First we went to the homepage for BLAST and you either choose protein or nucleotide blast, based upon which you’re looking for. Then you enter an accession number for the species you are searching for, as each has its own number. Then you open MEGA 4.0.2 and you open the Alignment Explorer/CLUSTAL. A box prompts you to “Create a new alignment”, and you either decide to build a DNA [yes] or Protein [No] sequence alignment. We chose protein alignments because that is what we are testing. After that, in MEGA 4 we chose the web query Genbank in order to search for the proper proteins to include in our cladogram. Now, we searched for either Tyrosinase or the 18sRNA. After this, we searched down the line of organisms for the specified organisms in our lists to be included in the cladogram. Once found, you press a button on the browser to “add to alignment”, which then adds it to the MEGA 4 application. Once all there, we selected all of them, and chose to “Align by ClustlW”. This aligned our sequences into corresponding matches to save as a MEGA data file. Next we “constructed a phylogeny Neighbor-Joining (NJ)” and selected a Bootstrap test of inferred phylogeny in order to produce the appropriate cladogram. Once we pressed compute, our cladogram appeared and this was the finale of the programs. 2) The graphical view shows the database sequences aligned to the query sequence. It gives you a quick idea of the overall quality of the matches and which regions of your sequence match the sequences in the database. The score of the alignment is indicated by colors. The descriptive view tells you about the sequence, the name, the organism from which the sequence came, the e-value, and in some cases a gene that is encoded by that sequence. The e-value shows you the likelihood a particular sequence will occur in the BLAST database by chance. Advantages of the graphical view is that you can compare one sequence to another very easily, advantages of the descriptive view is that you can quickly determine details about a particular sequence, that you would not be able to tell with a graphical view. Both of their disadvantages are the lack of the opposing advantages each offer. 3) You could easily search the BLAST database for matches of the protein sequence by name, or properties of the sequence. You can enter the sequence of the protein to find matches, even. Once matches come up you can analyze the various matches by creating a cladogram in MEGA 4. This would show you how long the sequence has been in existence and
Background image of page 1

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Image of page 2
This is the end of the preview. Sign up to access the rest of the document.

This note was uploaded on 03/15/2010 for the course BIO 49540 taught by Professor Robertfarris during the Spring '10 term at University of Texas.

Page1 / 5

Lab 5 - Paul Gonzales BIO 206L Session: 49540 Lab 5 1) Use...

This preview shows document pages 1 - 2. Sign up to view the full document.

View Full Document Right Arrow Icon
Ask a homework question - tutors are online