BLAST Lab

1. Open the Forward results file in a separate browser window
2. Copy ONLY one of your sequences (based on bird name)
3. Open http://blast.ncbi.nlm.nih.gov/Blast.cgi and select Human Genome
4. Paste your sequence into the query box.
5. Make sure MegaBlast is selected under “Program Selection” (it makes it much faster)
6. Launch the BLAST job and wait for the results
7. Record the statistics about the alignment in your lab notebooks.
   

   This summary is acceptable:
   

   >ref|NC_012920.1 Homo sapiens mitochondrion, complete genome
   Length=16569
   
   Score =   723 bits (391),  Expect = 0.0
   Identities = 398/401 (99%), Gaps = 1/401 (0%)
   Strand=Plus/Plus
   Reverse_sequence.fa.txt
   Query  8 to  408
   Sbjct  16012  to 16411
   

8. Repeat for your sequence in the Reverse results
9. Note the differences in the alignment location and strand orientation

Align your two sequences

1. open Align Sequences Nucleotide BLAST
2. copy and paste YOUR forward into the top query box
3. copy and paste YOUR reverse sequence into the bottom query box
4. Record the alignment as you did above noting any difference after the consensus begins

Results

Multiple Sequence Alignment

1. Open ClustalW2
2. Open the Forward results file in a separate browser window
3. Copy ALL of the Forward results of your sequences (based on bird name)
4. Paste into the field and make sure the sequence type is set to DNA
5. Click submit and notice the results
6. Note the bases where YOUR sequence is different than the consensus sequence (note there MAY be a button to print your results in color if so using that may make identifying the differences easier)
7. Download your sequence alignment
8. Repeat with Reverse sequence

Phylogeny

1. Open ClustalW2 Phylogeny
2. upload your sequence in the form and click submit
3. Examine the text based tree for the sequences which are more closely related
4. Record the sequence that is most closely related to yours