Our Services

Get 15% Discount on your First Order

[rank_math_breadcrumb]

Bioinformatics

  This assignment requires screenshots for the answers.

 

Query the NCBI database using the “GeneID” provided and obtain the FASTA formatted AQP7 protein sequences for:

Homo sapiens -> Human -> GeneID: 364 

Pan troglodytes -> Chimpanzee -> GeneID: 465043 

Mus musculus -> Mouse -> GeneID: 11832

Rattus norvegicus -> Rat -> GeneID: 29171

Bos Taurus -> Cow -> GeneID: 615498

Danio rerio -> Zebrafish -> GeneID: 334529

Canis lupus familiaris -> Dog -> GeneID: 474742

Sus scrofa -> Pig -> GeneID: 100126283

Equus caballus -> Horse -> GeneID: 100068324

Mustela putorius furo -> Ferret -> GeneID: 101683120

Mesocricetus auratus -> Hamster -> GeneID: 101837538

Myotis brandtii -> Bat -> GeneID: 102263763 

For the descriptive comment line found at the beginning of each sequence, replace the common name provided.  Paste/Copy below the sequences in the exact order listed above as your answer. 

Answer = ?

Question 2.

Using the sequences prepared as answer to Question 1, run the Clustal Omega tool (https://www.ebi.ac.uk/Tools/msa/clustalo/) to generate a multiple sequence alignment with “STEP 2” parameters set to “Pearson/FASTA”:

The Clustal Omega tool is a newer improved version of ClustalW2 multiple sequence alignment tool. Under the “Alignments” tab of the Clustal Omega output, copy/paste the unedited form of the alignment as your answer.

Answer = ?

Question 3.

Under the same “Results Summary” tab of the Clustal Omega output, click on the hyperlink found under “Percent Identity Matrix”. The identities in the matrix returned are those values used to “Guide” the order in which the multiple alignment was built. Copy/Paste this matrix as your answer.

Answer = ?

Question 4.

Under the “Phylogenetic Tree” tab of the Clustal Omega output, scroll down and provide a screen shot of the “Phylogenetic Tree”, which represents the “Guide Tree” for the multiple sequence alignment generated.

Answer = ?

Question 5.

What does the “overview” look like for your answer provided to Q2 using JalView?

Answer = ?

Question 6.

When you look at the “Overview” plot provided for your answer to Question 5, notice there appears to be some sequences in the alignment that have vertical gaps of missing color. When you look at the “Local” view, you will notice these sequences are dissimilar enough that they negatively impact the level of “Conservation” across the alignment. In turn, they should/can be removed. Which ones are they? 

Answer = ?

Question 7.

What does the MSA “overview look like after you remove the sequences identified in Q6? VERY IMPORTANT, be sure the sequences you have identified to be removed are the ones highlighted for removal before doing so. Inspect the PCA and the MSA to make sure that is the case before removing. If you have removed correctly, you should not see these sequences in your MSA afterwards.

Answer = ?

Question 8.

When looking over the answer to Q7, there may exist high “Conservation” now after deleting those sequences, but there are empty columns present. These are non-informative and need to be removed. What does the “overview” look like after removing these empty columns? VERY IMPORTANT, if you notice in your MSA that there appears to be a sequence still quite different than the rest, you need to go back to Question 6 and Question 7 and repeat.

Answer = ?

Question 9.

What are the final-now-edited sequences in the MSA at this point? VERY IMPORTANT, if you notice in your MSA what appear to be gaps in your sequence, you have not removed all outlier sequences and need to go back to Question 6, Question 7, Question 8 and repeat.

Answer = ?

Question 10.

When you have a MSA in FASTA sequence format, you can also ask and answer what the secondary structures (i.e., “H”elices, Beta Sh”E”ets) that may exist in the MSA are. What are these structures and where do they occur in the MSA?

Answer = ?

Share This Post

Email
WhatsApp
Facebook
Twitter
LinkedIn
Pinterest
Reddit

Order a Similar Paper and get 15% Discount on your First Order

Related Questions

LAb report

Please see the attached documents I have been done part of the report i need help to finish with plagarism report, please read the guidelines i have the sources there too.

Capital Budgeting

 Can someone help explain how to calculate the net present value (NPV) of a project with uneven cash flows over 5 years? [ slope] [[|slope]] [slope]() [slope]: <a href=””>slope</a> [url=]slope[/url] “slope”: [link= url]slope[/link]

forever new leather jacket

Discover eternal elegance with Foreverjackets.com’s forever new leather jacket. These jackets, designed for durability and style, provide a new touch on traditional fashion, making them suitable for every season and seamlessly improving your everyday outfit.

sdkjgslf

check file Jackson Hole Summit Ridge Ski Lodge – Warming Hut Monthly Income Report Jackson Hole – Income by Month January February March April May June July August September October November December Morning Meal 3500.21 3652.14 3456.74 3291.11 1109.09 534.36 415.12 379.85 401.25 479.27 1965.31 2987.22 Morning Snack 2250.31 3265.02

dis 555555555

  Should there be more of a focus on high school students selecting a career path while they are still in high school? Will this help them later on in life? Hinder them?  Is the career you are pursing now, what you were planning on in High School?  If so

Forensic Science Course in 2 weeks

My kid enrolled for Forensic Science Summer 2025 He finish first unit out of 5 unit but need urgent help to complete rest “online summer program” ASAP. The final deadline is 3-July-2025 to complete all works. Please check attached syllabus for complete course.

Resume Packet Questions

Answer Task 4-Questions 6-10, following the guidelines. Nothing else. This file is too large to display.View in new window

biology

Name: Date: Lab 1: Plant Structures, Reactants, and Products of Photosynthesis Activity 1: Label the reactants and products of photosynthesis 1. Launch the view · Launch Visible Biology. · Navigate to Study/Lab Activities, and find the Photosynthesis Lab section. · Select view 1. Photosynthesis. 2. Label the image below ·

What makes Geometry Dash special?

Geometry Dash stands out with its fast-paced rhythm-based gameplay, where precision timing and muscle memory are key to success. Its combination of vibrant visuals, catchy electronic music, and increasingly challenging levels creates an addictive experience that keeps players coming back. The ability to create and share custom levels adds unlimited

Prof Double R

 QUESTIONS 1 Where has healthcare information management been historically? How has the introduction of technology dramatically changed the landscape? How has the introduction of technology increased the need for and importance of proper management? Support your answer with relevant resources. QUESTIONS 2 A common misconception is that a nurse has

bel hav u6

attached Unit 6: Writing Assignment Due Saturday by 11:59pm Points 30 Submitting a file upload Unit 6 Writing Assignment Rubric Start Assignment Writing Assignment: Submit by Saturday 11:59 p.m. Prompt: Recall the implications from this week’s focus chapter on NAEP reading proficiency. Write a paper addressing each of the following

Dis

Chapter 2 This file is too large to display.View in new window

Paraphrase

I need help with paraphasing This file is too large to display.View in new window

Biology 2

1 2 PRE-LAB EXERCISES Open the A&P app, and from the left-side menu, select Cells and Tissue, and then choose Chapter 3. Cell Life Cycle. Use the modules to guide your exploration of the life cycle of cells. Be sure to use the book icon to learn more about the

Week 10 Bio

  Select two of the unit student learning outcome (USLO) prompts below to respond to in this week’s reflection. USLO 10.1 Differentiate normal body water and electrolyte composition and movement in the fluid compartments. USLO 10.2 Explain the regulation of water balance within the body. USLO 10.3 Explain the roles

Can this be done in 1 hour?

  This Journal is a 2-part one. Read about the “situation” below: During the first week of the semester, one of your friends, Mark Jefferson, is in an accident and is hospitalized. While still under the effects of anesthesia, he scribbles the following note for you to mail to his