ASSIGNMENT 6 (5%) - BLAST
BLAST Search:
Based on the sequence on the page 2, find the search result by using the link provided
(https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&BLAST_SPEC=OGP__96
06__9558&LINK_LOC=blasthome) and answer all the questions 1 - 4.
Use default parameter on the website for question 1 and 2. The link should direct us to the
interface as shown below. Please refer to the steps given.
Step 1: User should enter the given sequence in the box for Enter Query Sequence.
Step 2: Choose blastn for the program selection.
For Question 3 only Step 3: Click BLAST to get the results.
Step 1 Step 3 Step 2 1 Sequence:
GTGTCAATGTGTTTTGTGCTTATATTTTTCCTGCACTAAATTGAGGCATTATTTACTTT
CCAACGAGTGTATTGTGGTAAGTAAGGCCGACGTGATGAAATACATGTTATCGGCCC
CTGTGTTAAAAGGACGAATTGGGAAGTGGATTTTTGCCTTAACAGAGTTTGACCTCA
GATATGAATCGGCCAAAGCAGTCAAAGGACAAGCCCTGGCCGATTTCATTGTTCAA
CATAGAGACGAATCGGTTGCGTACGCAGATATTGTGCCATGGACATTGTATTTTGAT
GGATCCGTCTGCAGACATGGATGCGGTATCGGCCTAGTTATCATATCCCCTCGGGGG
GCAAGCTTTGAGTTTGCTTTTACTATCAAGCCTTATTACACTAACAATCAAGCAGAG
TACGAAGCGGTGCTTAAAGGCTTGCAGTTATTACAAGAAGTCGAGGCCGATTCCGTA
GAGATCATTGGTGACTCACAACTGGTAATTAATCAACTTTCTGGAGAGTATGAATGC
AAAGATGACATCCTCAAAGTCTACAATGAAGATTGCAAGGTGTTGTTTCAAGCATTC
AGGATCGTAACGATGAGGCATATACCCAGGAAGCAAAACTTCGAGGCCAATGACCT
GGCTCAGGGGGCATCGGGATACAGGCCGATGGCCAAGGGTGCACGAGTTCAAATTG
CCACCGTAGACGCCGACGATTGGAGATTTGCTATCATTGATTATTTGAAGAATCCTT
CCCAATCGGCGTCACGAAAGATGAAATACAAAGTATTGCAGTATGTCCTGTTAGATG
ATGATTTATACCATCGGATGATTGATGGTGTCTTGCTCAAGTGCCTAGGTCCTGAGG
AGGCCAGAGTCGTTATGAGCGAGGTCCATGCCTGATGCTA
Question 1: Give number of hits. (1 mark)
Question 2: Give the max identities of the sequence (%). (1 mark)
Question 3:
(a) Give the number of hits when the query subrange is changed (1 mark)
=1,
=28. (Refer interface given)
(b) Give one reason for the difference (if any) in term number of hits when searching the
whole sequence vs. 28 words size sequence. (1 mark)
2 Question 4:
Figure 1: Blosum62 Substitution Matrix QUERY L E N T F F V Q A N SUBJECT Y E N I T I I Q S N SCORE Based on the Figure 1 and table above, fill in the score by using Blosum62 Substitution Matrix. (1 mark) 3