Write the answers to questions (3) and (4) from Friday's lab blast demo in a file called hwk2/lab.answers.
Do a search of the SwissProt database using blastp using NP_001171499 (honeybee_gst.aa) saving the output in "tabular" format (-outfmt 6)
Repeat step 1, using the ssearch36 program specifying the BLOSUM62 matrix (-s BP62). (you can produce tabular output using the –m 8 option):
ssearch36 –s BP62 –m 8 honeybee_gst.aa s > output.file
For both the blastp and ssearch results, make a copy of each results file and remove all the lines with E() > 0.001
Write a bash script to isolate the library (subject) accession
information for each of the lines in the edited file, and save the
accession in a new file
For each accession, split it into its component parts (hit 'man cut' to see how to change the delimiter).
Write a script to save the accessions (P12345.3) to a file, and isolate only the accessions without the version information.
Compare the list of SwissProt accessions with E() < 0.001 from BLASTP and SSEARCH. Which program finds more homologs? For the program that finds fewer homologs, what are the E()-values of those hits in the list of hits from the other program?
Edit the copies of the original blastp and ssearch output files file to save the lines with 0.1 < E()-values < 2.0
For the accessions 0.1 < E() < 2.0, run the script from steps 4,5 to isolate the SwissProt accessions.
Then use the protein accessions to get the sequences from UniProt.
Write a script to take the accessions from with 0.1 < E() < 2.0 from the blastp search and re-search Swissprot for each of those accessions, saving the new search results in files named after the accession numbers.
Write a description of your work in the file "hwk2.notes", labeling the scripts that you wrote, and save the description, scripts, and results files in biol4230/hwk2.