Biological Sequences Analysis: Final Project Schedule: TBA. General instructions: the project is limited to 15 pages (references not included!), using double-spacing of lines and font 12. Projects not adhering to these guidelines will not be checked. Projects can be written in either Hebrew or English. You may hand in the projects in couples or alone. Each person/couple will have a project-guide (Nimrod or Dudu) which will be assigned to him/her. All questions/dilemmas/discussions should be forwarded to your guide, preferably by email, or by scheduling an appointment (by email ). In this project you will be studying a protein by using bioinformatics tools studied in the course. The protein will be assigned to you by your guide. You will also receive a research paper on this protein which will help you initiate your study. The project will be composed of the following stages: 1. Thoroughly read the paper you received about the protein. The purpose of this paper is to get you started: the paper will usually contain a short explanation on the function of this protein, references to other studies on the protein, and some sort of bioinformatics study on the protein. You are not necessarily expected to fully understand all the details of the study described in the paper, since it may contain terms you have not learned. The idea is just to give you a general feeling of what biological questions may be answered using bioinformatics tools regarding this protein. 2. Reading a general paper which describes the protein (preferably, a review on the protein if available), which you should find on your own (using PubMed or Google Scholar). This will help you get more acquainted with the protein, and help you write up the introduction to the project (but don't just copy it). 3. Using the bioinformatics tools learned in the course to study the protein. The most basic requirements are: (a) collecting sequences (you may use the accession numbers in the paper in (1) as a starting point, but don't go wild (if there are over 30 sequences, you may use only a subset) and creating a multiple sequence alignment, (b) creating a phylogenetic tree and performing an evolutionary analysis (Selecton and Consurf/Conseq). Other than that, you should try to use as many tools as possible in order to obtain as much valuable information as you can. Make sure you use the most suitable tool at each stage. All the above analyses will serve you to write the project. Throughout your writing you are to assume that we have no previous knowledge about the protein, and that we have not read any of the papers you have read on the subject. The structure of the project should be similar to a published paper, which is composed of the following chapters: 1. Introduction – in this section you are required to describe the protein, its function, and whatever is currently known about it in the literature.(20 points) 2. Methods – shortly describe the methods you used in the study. This should be similar to the "Methods" section in a published paper, such as the one read in (1). This means that anyone who wishes to reproduce your study, will be able to do so by reading this section.(20 points). 3. Results – in this section, you are required to describe and display the results you obtained (from (3)). Only meaningful results should be presented. For example, there is no need to display the full MSA – only MSA of interesting regions. This guideline also applies to figures. This basically means that you are responsible for defining what is interesting in your work. (20 points) 4. Discussion – this section should include an integration of your results, their implications. (20 points) 5. Future Research – in this section you should raise ideas for future research (bioinformatics and/or non-bioinformatics). Sections 4 and 5 are the place where you are required to display creativity. (10 points) 6. References – please adhere to any style used in a published paper (such as papers of PNAS, Nature or Science journals) (same goes for citations throughout the paper). Make sure the references are exact, consistent and in the same format throughout the whole project (10 points). ± 10 points: general impression of the quality and creativity of the project Enjoy and good luck!