Analyze the conserved domains in your protein

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Reference no: EM131479638

Do a research on gene RASA1. Read the instruction to know what is required

Introduction

Your final project will center around the gene that you chose, and use bioinformatics tools to study these genes. Your theme of the final paper is exactly the same as the course: use bioinformatics to add biological knowledge.

Outline of your paper:

1. Introduce the biology of your gene/protein. You can discuss genetics, evolution and conservation, intron-exon structure, splice variants, and isoforms, phenotypes (if known) such as human diseases or developmental defects, and the biochemical protein function (receptor, kinase, signaling molecule, motor protein, etc). This information will come from NCBI Books, OMIM, review papers, and primary research literature. Be sure to cite and reference your sources just like in any other university course.

2. The core of the paper is your bioinformatic analysis of these genes. You need to include the following:

(a) BLAST to find orthologs and paralogs. Discuss the evolutionary history of your gene/protein.

(b) Do a T-COFFEE/MUSCLE/MAFFT/CLUSTAL/etc multiple global alignment over homologues, and analyze the results.

(d) Produce a phylogenetic tree of homologues, including an outgroup. Analyze the resulting phylogeny.

(e) Study the three-dimensional protein domain structure based on existing crystal structures (in PDB) and/or homology modeling (Phyre). If there are known important mutations in that domain (e.g., from OMIM), show those loci in the figure. Similarly, if there are some highly conserved loci in that protein, definitely show them in the figure.

(f) Analyze microarray data and protein-protein interaction networks.

Feel free to use and include additional bioinformatics tools you find on your own.
For these analyses, fully document how you performed the analysis. For example, include the following for each type of analysis:
- Web site and tool used to perform the analysis
- Parameter settings, for example, BLAST algorithm, database, substitution matrix, etc.

3. Finally, and most importantly, explain how your bioinformatic results add biological
knowledge to the story. Be sure to address uncertainties such as incorrectly inferring homology from sequence similarity, and how a follow-up study could increase the strength of your evidence.

4. References.

5. Bioinformatics tool outputs. Put text and images from bioinformatics tools here.

Attachment:- Outline and sample.rar

Reference no: EM131479638

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Reviews

len1479638

5/1/2017 1:35:51 AM

• The file must be in .docx, .doc, or .r tf format. • The paper length must be at least five full pages. • The format must be single spaced, 12 point Times Roman, 1-inch margins all around. Put a single blank line between paragraphs, and don’t indent paragraphs. • The minimum page count does not include the Reference section or computer output from bioinformatics tools. • Put all the computer output and the Reference section at the back of the paper, not in-line with the text. • You can choose any reference format such as APA or MLA, but you use it consistently throughout. One easy option is to copy references directly from PubMed.

len1479638

5/1/2017 1:35:35 AM

If the paper is less than the minimum required size (big font, big spaces between lines, big margins, too few pages, etc), the maximum grade will be scaled accordingly. In these cases, we run software over your paper to reformat it correctly, and determine the amount that is actually written, and then scale from there. For example, if after correct reformatting, your paper is 3 pages, then the maximum possible score would be 3/5 × 100 = 60, and that’s if everything in those 3 pages is absolutely perfect. • We’ d much rather see everyone doing outstanding work and give ever yone an “ A” . We really want to hand out those A grades, but you have to help us.

len1479638

5/1/2017 1:35:27 AM

• Feel free to discuss your research with any other students, biologists, labmates, TAs, or professors, but all writing must be your own. • Copying/pasting unattr ibuted text from the web is absolutely plagiar ism and guarantees an “ F” . • All final papers are run through a plagiarism checker, which checks all of PubMed, all of the web, and previous students’ papers. Let’s not go down that path. . . • Quoting text with a proper citation is legal but will get low grades. We want your thoughts, ideas, words, and analyses, not another author’s. • Be sure the paper meets the minimum size requirements. If you produce more, you will improve your chances of getting a top grade.

len1479638

5/1/2017 1:35:08 AM

Read the doc named"Final Paper Insturctions" For this assignment, do a research on gene RASA1! Read the instruction and look at the sample paper to know what is required! Look at the sample outlines to get an idea of what's required. Also, include a sequence analysis for this gene in the paper ! And it's due next tuesday. For the ZIp File, comments as under: I have attached the project instruction one more times along with the sample paper and the sample outlines. Read the doc named"Final Paper Insturctions" For this assignment, do a research on gene RASA1! Read the instruction and look at the sample paper to know what is required! Look at the sample outlines to get an idea of what's required. Also, include a sequence analysis for this gene in the paper as an extra credit as I need !

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