Individual Project details are available inside our class folder on pitt.box.com. This page contains writing tips for your projects, as well as a Frequently Asked Questions section below.
Project Version 1:
Do you want any kind of citations for the info I list for my three proteins?
- No - citations are only required for version 2 & beyond.
Project Version 2:
How should we source the articles we are citing?
- I don't have a particular style requirement, but for a nice one see: http://pitt.libguides.com/BIOSC1540
- Writing & Citing ==> Online Guide to CSE Citation Style
How many sequences are we supposed to record and put in sheet 1 of the Excel file?
- At this point, sheet 1 should have exactly the number of sequences your .msf file contains, and each row should provide more info about each. (i.e.: name/species/etc)
What should be on the 2nd page of the Excel Spread sheet? Just a sequence, this is what you mean by "hit table text" in NCBI, for instance?
- I'm looking for a summary of your matches (hits) from the blast search
- A "hit table" is the line-by-line list of the best matches - each row having name/score/e-value.
- The sheet shouldn't contain any actual sequences or pairwise alignments
- See our BLAST lab for info on how to do this.
I've saved my multiple sequence alignment as a .msf file. When I try to open it, my Mac says "cannot open, as there is no application to open it".
- Most of the files for this class won't open by double-clicking. You'll have to start the program first, and use its File menu to choose/open your file.
Project Version 3:
You mention that we shouldn't be starting from scratch and will be adding to and editing our version 2 document. Does that mean I should just take what I wrote for version 2, fix it up to match the current project, add the new material, and that should be good?
- Yes, exactly.
When I searched for some of the vertebrate species (from the list you posted in the Appendix), it said there were 0 hits corresponding to that species.
- First off, if you were using the Taxonomy Browser, try downloading your results in Excel format instead (see current version of project instructions for details). If you are still unable to find any, just make sure to mention this in your report.
I was trying to figure out the scoring matrix for the rcsb/PDB search and I saw "compositional matrix adjustment," is this the correct scoring matrix?
- On your text results, see the very top and very bottom for info on the search program, database, & scoring matrix
In the Excel section, what does "sheet 7 (pdb)" refer to?
- This refers to the results you obtained from the project's Assignment #8 (search for any solved 3D structures similar to your query)
For the Background, what does "immediately upstream/downstream of your protein" mean?
- I'm not referring to DNA or protein sequence here, but rather the sequence of molecular events your protein is a part of. Upstream would refer to the final event/molecule that "activates" your protein (phosphorylation, release from inhibition, binding to partner, etc), while downstream would refer to the first molecule/event your protein triggers toward performing its function. Things can tend to get complicated with the array of different avenues/signals that can start the sequence of events, and again in the array of avenues/signals that are ultimately triggered. For your project (& your sanity), I'd like you to mainly focus on the other proteins/molecules that your protein directly interacts with.
Extra
Credit
Additional points will be awarded to your project grade if you discover during the course of your project that either:
Last Updated: 23 May 2016
Question or Comments: epolinko@pitt.edu
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