Bioinformatics_lab_HANDOUT_and_worksheet 2020.doc – BIO214 Lab9 Bioinformatics Lab Assignment(20 pts Name BIOINFORMATICS Biological information is

BIO214
Name:___________________________
Lab9:
Bioinformatics
Lab Assignment (20 pts)
BIOINFORMATICS
Biological information is encoded in the nucleotide sequence of DNA.
Bioinformatics is the field
that identifies biological information in DNA using computer-based tools. Some bioinformatics
algorithms aid the identification of genes, promoters, and other functional elements of DNA.
Other
algorithms help determine the evolutionary relationships between DNA sequences.
Because of the large number of tools and DNA sequences available on the Internet, experiments
that are done on the computer now complement experiments done
in vitro
and
in vivo
. This
movement between biochemistry and computation is a key feature of modern biological research.
In Part I, you will use the Basic Local Alignment Search Tool (BLAST) to identify sequences in
biological databases and to make predictions about the outcome of your experiments. In Part II,
you will find and copy the human PTC taster and non-taster allele DNA sequences. In Part III, you
will discover the chromosome location of the PTC tasting gene. In Part IV, you will explore the
evolutionary history of the gene.
Answer all questions that are marked in bold.
I.
Use BLAST to Find DNA Sequences in Databases
The following primer set was used in the experiment
5’-
CCTTCGTTTTCTTGGTGAATTTTTGGGATGTAGTGAAGAGGCGG
-3’ (Forward
Primer)
5′-
AGGTTGGCTTGGTTTGCAATCATC
-3′ (Reverse Primer)
1. Initiate a BLAST search.
a.
Open the Internet site of the National Center for Biotechnology Information (NCBI)

.
b.
Click on the BLAST link in the “Popular Resources” list on the right side of the page.
c.
Click on the link nucleotide BLAST under the heading Basic BLAST.
d.
Where it says “NCBI/BLAST/blastn suite” be sure the “blastn” tab is selected
e.
Enter the sequences of the primers into the Search window. These are the query
sequences.
It may be easiest to cut and paste them from this document rather than
typing them by hand.
Paste these sequences one right after the other into the query box
(where it says “enter accession number, gi, or FASTA sequence”), no spaces needed.
f.
Omit any non-nucleotide characters from the window, because they will not be
recognized by the BLAST algorithm.
g.
In the “Choose search set” section, under database, select “others (nr etc)” and in the
drop down list directly below this, select “Nucleotide collection (nr/nt)”
h.
Under Program Selection, optimize for somewhat similar sequences by selecting blastn.

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