Finding transcribed genes in R. williamsianum

Now that you know how to use BLAST on the command line, we can use it to look for interesting things.

Key among these are:
mRNA transcripts
RAD-sequencing from other species

I've put the necessary things on both new iMacs, and you can give it a try.

Open the file input.fasta, replace with your sequence in fasta format. Save the file.

Open Terminal.

cd RNA_seq

./blastn -query input.fasta -db Trinity_GG -task blastn -outfmt 7

Look over your blast hits. How many transcripts exist?

To get the fasta sequence of blast hits you're interested in:

python getFasta.py Trinity_GG.fa

Then paste in the sequence name, and copy out the result.

Undergraduate Research Symposium

We won't meet this week, make sure to stop by the Undergraduate Research Symposium to check out posters and presentations.

Shayna: Local Processes of Genetic Recombination in Populations of Rhododendron macrophyllum

11-12:30, MGH Commons West, Easel 24

Kate: Fungal Symbionts in Genus Rhododendron: Evaluation of Ericaceous Mycorrhizal Relationships

3:45-5:15, JHN 111 (She'll probably go at 4:30, but schedule is up to the moderator)

Willy: Underreported Inflation Rates in Argentina: Using the Right Numbers to Study the Effects

3:45-5:15, MGH 234 (He'll probably go at 4:30, but schedule is up to the moderator)

BLAST

NCBI BLAST - Basic Local Alignment Search Tool

Find regions of local similarities between sequences

http://blast.ncbi.nlm.nih.gov/BlastAlign.cgi

Step 1:
Download blastn executable, blast database, and input file:
https://docs.google.com/file/d/0B12A3agEjLOMajJYUUV6WmhVWms/edit?usp=sharing


Step 2:
Move these files to folder you like. Either through command line or drag and drop.
mv ~/Downloads/blastn ~/Desktop/folderyoulike/blastn
cd ~/Desktop/folderyoulike

Step 3:
Change file permissions:
chmod 755 blastn

Step 4:
Do a blast search:
./blastn -db scaffold_6 -query ty1copia_element.fa

CENSOR

Find regions matching curated repeat elements

http://www.girinst.org/censor/index.php