BIOL 357 – What are four ways to search within an individual

Subject: Biology / General Biology Question
Question 1 (4 points)
What are four ways to search within an individual Entrez database?
(a list with bullet points with summary titles is fine)

Question 2 (1 point)
For a class assignment, you are asked to conduct a query in BLAST using a
sequence of mouse DNA. As part of the question, you also need to determine if
your given genomic sequence is transcribed into a mRNA sequence.
Which BLAST data base is the best to use for this scenario?
a. nr BLAST
b. protein BLAST
c. Mouse G+T Blast
d. refseq_genomic

Question 3 (1 point) After conducting a BLAST search, your results show the following image.
In the image below, which sequences would you select to refine your search to
only examine those that are most similar to your sequence?
(the order of the color of bars from top to bottom are: red, purple, green, blue,
and black)
a. red and blue
b. purple and black
c. green and black
d. red and purple

Question 4 (2 points)
In a few sentences, explain why searching through a highly curated database
such as RefSeq has advantages over searching through general gene databases
(like Blast or various non-specific Entrez) when starting with a single known
gene.

Question 5 (1 point)
What is a genome?
(choose all that may apply)
a. Chloroplast DNA
b. Chromosomal DNA
c. Mitochondrial DNA
d. Vacuole DNA

Question 6 (2 points)
Give an example when you can use Ensembl to answer a question in
bioinformatics.(1-2 sentences)

Question 7 (1 point)
Molecular phylogeny is the study of evolutionary relationships based on
molecular sequences and _______. a. Similarities in morphology
b. Multiple Sequence Alignmens
c. Protein function
d. Genome trees Question 8 (1 point) Use the phylogeny below to answer the question.
Of the organisms on the tree, which two (from the selections below) can we say
share a recent common ancestor that the other organisms do not share.
a. Pine and Rose
b. Moss and Rose c. Fern and Rose
d. Fern and Pine

Question 9 (1 point)
Which type of characteristics (DNA sequence element or a physical
characteristic) can be found in different organisms that are similar because the
characteristics were inherited from a common ancestor that also had that
characteristic? a. Analogous charactistics
b. Homoplasious characteristic
c. Homologous characteristic
d. Paralogous characteristic

Question 10 (1 point)
In testing the robustness of a phyogenetic tree, a researcher may use a test that
relies on random sampling with replacement to develop alternate phylogenetic
trees to determine the confidence in the relationships on the tree. What type of analysis is this? (one word or a short sentence is all that is
needed)

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