BLAST results

If your BLAST run did not complete, you can download the output files:

Fly versus worm Worm versus fly

There were run with default parameters, output_fmt 6 and culling_limit 1

Additional help learning Linux shell

Some of you have requested additional resources for learning the shell. Here are two:

  1. An online tutorial at Code Academy. While it is in bash, almost everything will be applicable to fish.
  2. A CheatSheet that provides a quick reference of Linux commands.

Assignment 1 Update

Assignment 1 is now due Monday April 17, 1pm

Gina has office hours Thursday at noon and Monday at noon.

You can skip the z-score question, but if you want to calculate it, you could cut and paste into an online calculator to get the standard deviation scores

How to turn in your assignments

I have created a github repository for each of you for this assignment.

To turn in this assignment first go to and find the repository for this week. You may need to go to the UCDBIS180L-17 website. It will be something like Assignment_1_Maloof.Julin. Find the clone link and clone it to your computer.

git clone YOUR_URL

Then cd into the repos, mv your assignment files(s) into the repository, add, commit, and push!

mv ./
git add
git commit -m "added Assignment 1 documents"
git push

You will need to adjust the file paths as appropriate for your system. Also include your Markdown lab notebooks.

For future assignments the repository for the assignment will be available as we start the lab. I strongly recommend that you clone the repository immediately, do your work in the repository, and commit and push as you go. This will provide you a backup of your work, should your AWS instance fail.

Markdown Tables

The lab exercise for sequence alignment asks you to make a Markdown table. But how do you make one?

The basic format is like this:

| header 1 |  header 2 | header 3|
| data 1.1 | data 1.2 | data 1.3      |
|  2.1 | data 2.2     |  2.3  |

which produces

header 1 header 2 header 3
data 1.1 data 1.2 data 1.3
2.1 data 2.2 2.3

You use pipes | to denote the columns, and separate the headers from the data with a row of |--|

You can use colons in the header separating row to left or right (or center) justify. Look at columns 1 vs 2 vs 3 in the table.

Note that even if the spacing in your table is uneven (pipes don’t line up) the table still looks good in the output. (But try to make it like nice even in the unformatted text)

For more details, see here. For tool to help you geneate a table without all of that finicking typing, see here