What type of organism is this?

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Theses questions every easy. All information in the PDF.
BLAST Website:
https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE…
Lab 23: Bioinformatics
New techniques in DNA sequencing have lead to massive amounts of sequence data. These data have led scientists create new tools and disciplines, including bioinformatics. Bioinformatics attempts to use sequence data to help answer questions about biology.
What is sequence data?
Sequence data is the order of nucleotides in a DNA molecule, or the order of amino acids in a protein molecule. For example, the sequence below is DNA sequence data. Note that only the bases are listed, since the sugar and phosphates are the same for every nucleotide.
ttacccttcttttgtcgtgccctgcgcccgcgttaccggcactggcagccaggcgcgaat
Below is protein sequence data. The single letters stand for individual amino acids. Note that the side chains are the only parts listed.
MRRLRFSPRSSFARTLLLIVTLLFASLVTTYLVVLNFAILPSLQQFNKVLAYEVRMLMTD
Where is the sequence data?
Sequences are stored in a computer database that can be accessed via the internet. The largest public database of sequences is in the US, and is maintained by the National Center for Biotechnology Information, which is part of the National Institute for Health. The sequences are contained in a database called GenBank, and can be searched by a program called Basic Local Alignment Search Tool (BLAST). Searching for sequences is called “blasting” like searching the internet is called “googling,” However, it is important to remember there are other alignment programs and databases, just like there are other search engines.
What does the program return after a search?
When a person inputs sequence into the search program, the program uses an algorithm to look in the database for the best matches to the submitted sequence. The matches are aligned with the submitted sequence. This means the sequence that was put into the search is lined up with the sequence found in the database. Information about the matches is also displayed. For our exercise today, there is only one important piece of information you need from the aligned sequence, the identity of the organism that contains the sequence. The identity of an organism is its Latin name that is composed of its genus and specific names. For example, you are a specimen of Homo sapiens. Your genus is Homo and your specific epithet is sapiens. Let’s say BLAST returns aligned sequences, and the top hit is “Bacillus subtilis KCTC 1028, complete genome.”
1. What is the Latin name of this organism?
2. What type of organism is this? Use the Latin name to search the internet if you do not know.
What is a sequence alignment?
Below is an example of a sequence alignment. The sequence on top is marked “Query” as it is the sequence that was submitted to BLAST while “Sbjct” is the sequence that BLAST found in the database and aligned it with the submitted sequence. Note the gaps where the nucleotides do not match.
What can you do with sequence data?
Sequence data can be used to investigate evolutionary relationships. Sequences from closely related species should more similar than those from distantly related species. When sequence is submitted to BLAST, the algorithm ranks the hits by putting more similar sequences at the top. As you scroll down the list of hits, you move to sequences from more distantly related organisms
Sequence data can be used to investigate functional relationships. Let’s say a researcher is studying a particular protein, but doesn’t know what it does. Using the sequence of their gene, they can search databases (DNA or protein) for similar sequences in other organisms. If they find a protein with a very similar sequence (or similar regions) whose function is known, they can make a guess that their protein of interest functions the same way. This guess is often a good place to start, but all guesses must be confirmed by research in a laboratory.
Activity – Solve the Murder
Equipment: Internet
There has been a terrible murder at the Zoo. A male lion was found dead, battered, and covered in blood. You are working in a crime lab and recieve two blood samples from the scene of the crime.
You isolate the DNA and determine the nucleotide sequences from both samples. The sequences are listed below. Use nucleotide BLAST to determine which organisms the blood came from. Use the Latin names to search the internet for the common names of these organisms.
Sample A TTGCATGGTGATTTCCTTAGTGTCGCTACCCAAGCCTTATTCATCTTAACTGTACTATTA
Sample B GATCGTATTTATGCAATGAAAGTTGTGAAAAAAGAGCTTGTCAATGATGATGAGGTAAGCA CAATGATGC
3. Who do you think is the murderer?
Activity – Sequence Safari
Equipment: Internets, 1 4-sided die, 1 20-sided die
Now we are going randomly create a piece of DNA and pretend that it is our sequence of interest. Use the 4 sided die to randomly generate a sequence of 20 nucleotides by rolling the die and writing the 1 letter code. Use the table to the right. For example, if you roll a one, you write down an A.
4. Write the sequence of 20 nucleotides in the space below.
Now use nucleotide BLAST on your sequence. Find the name of the organism with the highest score. It will be in Latin (genus and species).
5. Write the genus and species name of your organism
6. What type of organism is this? Use the Latin name to search the internet if you do not know.
Next we will randomly generate a protein using a 20-sided die and the table below. Roll 20, 20-sided dice to generate a peptide of 20 amino acids.
7. Write the sequence of 20 amino acids in the space below.
Now use protein BLAST on your sequence. Find the name of the organism with the highest score.
8. Write the genus and species name of your organism. If you did not get a match, say so.
9. What type of organism is this? Use the Latin name to search the internet if you do not know.
Questions
1. Only the bases are listed in DNA sequence data. Why aren’t the sugars and phosphates listed?
2. Who curates the largest public database of biological information?
3. How does a database of sequences help researchers around the world?
4. Why do you think it is harder to create synthetic protein sequences and find matches in the database than it is to create synthetic nucleotide sequences and find matches in the database? What is different about protein sequence data?
Glossary
Algorithm
A process or set of rules to be followed in calculations or other problem- solving operations, especially by a computer.
Bioinformatics
The storing, retrieving and analyzing of biological data, such as nucleic acid and protein sequences. It can also be used to study pathways, genetics, and protein structure and function. A computer heavy discipline it also employs databases, the internet, and algorithms. Bioinformatics is sometimes called in silico biology because experiments can be performed via computer.
Database
A structured set of data held in a computer, esp. one that is accessible in various ways.
Genome
All of an organism’s hereditary information or DNA

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