Sequences (HIV-1 protease)[]
HIV protease cDNA sequence (FASTA)[]
>ENA|CAA09312|CAA09312.1 Human immunodeficiency virus partial HIV-1 protease : Location:1..297 CCTCAGGTCACTCTTTGGCAACGACCCATAGTCACAATAAAGATAGGGGGGCAACTAAAG GAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGA AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT CAGGTATCCATAGAAATCTGCGGACATAAAGCTATAGGTACAGTATTAATAGGACCTACA CCTGTCAACATAATTGGAAGGAATCTGTTGACTCAGCTTGGCTGCACTTTAAATTTT
HIV protease amino acid sequence (FASTA)[]
>gi|25121906|ref|NP_705926.1| retropepsin [Human immunodeficiency virus 1] PQVTLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHK AIGTVLVGPTPVNIIGRNLLTQIGCTLNF
Instructions[]
MMG 240, 11 Feb 2014
Note: Recent blast searches and their results will be automatically saved and easily accessed if you set up and sign into a free MyNCBI account
——
N1: Nucleotide search 1
(1) Query sequence is the FASTA nucleotide sequence here on John’s Wikia page.
(2) Go to NCBI-BLAST home page
(3) Select nucleotide blast (this is also termed blastn)
(4) Copy and paste the FASTA sequence above into Query Sequence box on the blastn page
(5) Under Choose Search Set, select Reference genomic sequences
(6) Under Program Selection, choose blastn
(7) Check Show results in a new window at the bottom of the page
(8) Hit BLAST button. Be patient, as this is an enormous search and will take a few minutes
(9) Examine the table of search results. Note particularly the Query coverage and E value
(10) Select sequences of interest and generate alignments by clicking the multiple alignment button
(11) Explore your results and make use of two links at the top of this page: How to read this page, and Blast report description
——
A1: Amino acid search 1
(1) Query sequence is the FASTA amino acid sequence here on John’s Wikia page.
(2) Go to NCBI-BLAST home page
(3) Select protein blast (this is also termed blastp)
(4) Copy and paste the FASTA sequence above into Query Sequence box on the blastn page
(5) Under Choose Search Set, select Reference proteins (also known as refseq protein)
(6) Under Program Selection, choose blastp
(7) Check Show results in a new window at the bottom of the page
(8) Hit BLAST button. This search will be much faster than A1 above.
(9) Examine the table of search results. Note particularly the Query coverage, E value, and Identity. Always ask yourself if these results make biological sense.
(10) Select sequences of interest and generate alignments by clicking the multiple alignment button
——
Assignment
(1) Repeat search N1 for the nucleotide sequence encoding your protein. Explore different strategies for narrowing or expanding your search, if appropriate. These results will be useful for your wiki page on Molecular biodiversity and evolution
(2) Repeat search A1 for the amino acid sequence encoding your protein. Explore different strategies for narrowing or expanding your search, if appropriate. These results will be useful for your wiki page on Molecular biodiversity and evolution