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sr320 / course-fish546-2021

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Using Jupyter and Blast #10

Closed sr320 closed 3 years ago

sr320 commented 3 years ago

This week you will use Blastx to compare a set of unknown nucleotide sequences to a known set of protein sequences.. specifically the Swiss-Prot sequences at https://www.uniprot.org/downloads.

Unless you already have a fasta use http://eagle.fish.washington.edu/cnidarian/Ab_4denovo_CLC6_a.fa

Show all of your work in Jupyter notebook that you push to the GitHub repo you created last week.

hints ... https://github.com/sr320/fun-gen/blob/master/Jupyter/03-Local-Blast.ipynb AND this screen recording

Please add URL to your Jupyter notebook below once on GitHub.

aspencoyle commented 3 years ago

Finished - here's my Jupyter notebook!

skreling commented 3 years ago

https://github.com/fish546-2021/Sam-Metabarcoding/blob/main/Running_blast_in_Jupyter.ipynb

laurel-nave-powers commented 3 years ago

https://github.com/fish546-2021/Laurel-genes/blob/main/0120-blast-quiz.ipynb

I think I've run into an issue with the last part when running blastx. My computer just keeps spinning and working on it endlessly and never puts out any output.

jdduprey commented 3 years ago

Joe's blast practice

meganewing commented 3 years ago

https://github.com/fish546-2021/Megan-project/blob/main/0120-blast-quiz.ipynb

Holy heck, the last 3 commands took so long for my computer to finish. I started running them at 8:30!!! They just now finished lol

Brybrio commented 3 years ago

https://github.com/fish546-2021/Bryan-Eelgrass/blob/main/BABO-Blast-Practice.ipynb