Science Homework Help

Genbank is a genetic sequence database of all publicly available DNA sequences.

How to access:

URL: http://www.ncbi.nlm.nih.gov/genbank/

Or Google Genbank and select the first link

Step 1: Choose the appropriate search category from the drop down menu next to the search box. (For this activity we will use the nucleotide option).

Step 2: Search a specific nucleotide using the Genbank accession number (example: AF196646) found in the dolphin herpesvirus article on Eres. (Proliferative Dermatitis associated with a novel alphaherpesvirus in an atlantic bottlenose dolphin (Tursiops truncates))

Step 3: Click on the FASTA link for access to the DNA sequence of the particular herpesvirus.

Step 4: Copy and paste the FASTA into a text editor file to use in phylogenetic tree building software.

*Step 5: Paste sequences into MEGA alignment software and examine conserved and variable regions. Try this in both DNA and translated sequences.

Assignment: follow these steps and limit your search to one clade/group of virus sequences ( be specifc minimum is half page – 1 pg for question, double spaced. ) you may include any fingers or tables that would present any data or findings etc. * fingers go at the end of all of the writing.

1. What vertebrates have been reported to be infected by this viral strain?
2. Build a FASTA File and then import the sequences into an alignment program so you can see all of the vertebrate hosts and the viral DNA sequence isolated from them. Be sure you keep track of all the sequence files that identify where the sequence came from (this is information you can get from NCBI).
3. Identify regions that are conserved and variable among the compared sequences. How big are these regions? How many of them are there?
4. What are the implications for transmission if strains are very
5. relevant papers : https://s3.us-east-1.amazonaws.com/blackboard.lear… https://s3.us-east-1.amazonaws.com/blackboard.lear… https://s3.us-east-1.amazonaws.com/blackboard.lear… https://s3.us-east-1.amazonaws.com/blackboard.lear…