HW 1B Thread
Please put questions regarding HW1B in this thread.
- Note: minor update of HW1b. I added a link to Robert Edgar's review of multiple sequence alignment in Current Opinion in Structural Biology, and clarified that you also want to include the first row and column for the optimal score matrix.
7 Comments:
You also want to add the first row and column of the optimal score matrix - for what? Which part of the assignment is this? Thanks!
-Daniela
This is for question 3; I changed the score matrix dimensions to (M+1) x (N+1).
Can you give us some instructions on how to find the snp that causes sickle cell? thanks
I tried this (which may be inefficient):
- search Entrez Gene for sickle-cell anemia
- focus on the first record which is human HBB hemo-globin
- use the OMIM link in the Entrez record for HBB hemo-globin
- browse the Allelic Variants of OMIM record and find that .0038 HEMOGLOBIN C [HBB, GLU6LYS] is related to sickle-cell anemia
- I also used the SNP link in Entrez Gene record to get further information on this SNP
Does anybody know how to find the nucleotide sequence given the protein sequence for 3.d?
Also, for 3.c I don't get any "visuals" - I get "
No significant similarity was found" and some other data... Anybody get visuals, and how?
Thanks!
Katrin
For 3(d)
- search Entrez Genome for Ecoli K12 (or NC_000913 directly)
- At the summary page for NC_000913, click the link "Protein Coding: 4243" for a table of protein coding sequences
- In that table, locate the row(s) with Gi 90111240 (Gi 16131163). At the end of row(s), click the little orange diamond for FASTA format of the DNA sequence
For 3(c), I think you just need to try out the bl2seq program (using their defaults) and then visually compare the alignment by bl2seq with yours.
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