PLEASE SOMEONE HELP!!!! The following problems involve using the Basic Local Ali

Question

PLEASE SOMEONE HELP!!!!

The following problems involve using the Basic Local Alignment Search Tool or BLAST. Using NCBI’s BLAST search page answer the following:

http://blast.ncbi.nlm.nih.gov/Blast.cgi

Remember:

1) Choose the non-redundant or “nr” database to access non-human, non-mouse genome data.

2) E value: a negative value or zero is the best value

3) Some proteins have a putative conserved domain which can be accessed by a protein blast.

Problem 1:

Using this DNA (nucleotide) sequence answer the following questions:

àATGAAATTCACGATTCAAAAAGATCGTCTTGTTGAAAGTGTCCAAGATGTATTAAAAGCAGTTTCATCCA GAACCACGATTCCCATTCTGACTGGTATTAAAATTGTTGCATCAGATGATGGAGTATCCTTTACAGGGAG TGACTCAGATATTTCTATTGAATCCTTCATTCCAAAAGAAGAAGGAGATAAAGAAATCGTCACTATTGAA CAGCCCGGAAGCATCGTTTTACAGGCTCGCTTTTTTAGTGAAATTGTAAAAAAATTGCCGATGGCAACTG TAGAAATTGAAGTCCAAAATCAGTATTTGACGATTATCCGTTCTGGTAAAGCTGAATTTAATCTAAACGG ACTGGATGCTGATGAATATCCGCACTTGCCGCAGATTGAAGAGCATCATGCGATTCAGATCCCAACTGAT TTGTTAAAAAATCTAATCAGACAAACAGTATTTGCAGTGTCCACCTCAGAAACACGCCCTATCTTGACAG GTGTAAACTGGAAAGTGGAGCAAAGTGAATTATTATGCACTGCAACGGATAGCCACCGTCTTGCATTAAG AAAGGCGAAACTTGATATTCCAGAAGACAGATCTTATAACGTCGTGATTCCGGGAAAAAGTTTAACTGAA CTCAGCAAGATTTTAGATGACAACCAGGAACTTGTAGATATCGTCATCACAGAAACCCAAGTTCTGTTTA AAGCGAAAAACGTCTTGTTCTTCTCACGGCTTCTGGACGGGAATTATCCAGACACAACCAGCCTGATTCC GCAAGACAGCAAAACAGAAATCATTGTGAACACAAAAGAATTCCTTCAGGCCATTGATCGTGCATCTCTT TTAGCTAGAGAGGGACGCAACAACGTTGTAAAACTGTCCGCAAAACCGGCTGAATCCATTGAAATTTCTT CCAATTCGCCAGAAATCGGTAAAGTTGTGGAAGCAATTGTTGCGGATCAAATTGAAGGTGAGGAATTAAA TATCTCTTTTAGTCCAAAATATATGCTGGATGCACTAAAGGTGCTTGAAGGAGCAGAAATACGCGTAAGC TTTACAGGCGCAATGAGACCTTTCTTAATTCGCACGCCGAATGATGAAACGATTGTACAGCTTATCCTTC CTGTCAGAACCTATTAA ß

1.1 Can you tell which end is the 5’ end? Why?

1.2 Perform a nucleotide blast or BLASTn search of the DNA but only use the first eight rows of bases. What was your top hit? Also record the E-value.

1.3 Now perform BLASTn with the entire sequence and compare this result to the

previous search. Explain what happened to the e-value and why?

1.4 Using the complete DNA sequence perform a BLASTx search. What is the best match now? Record the E-value.

1.5 What is the difference in the BLASTn and BLASTx results?

Explanation / Answer

1.1) "àATG" end is 5' end because it starts with a star codon which is usually present in a gene. The the end (3') there is also a stop codon that completes the open reading frame.

1.2) The top hit is "Bacillus subtilis strain FB6-3 chromosome" (accession number, CP032089.1). The E-value is 2e-139.

1.3) The top hit is "Bacillus subtilis strain NCIB 3610 chromosome, complete genome" (accession number, CP020102.1). The E-value is 0. The E-value decreased from 2e-139 to zero because the score of the match was increased in case of full sequence. As small sequence have greater chance to be found in the database as compared to large sequences, the probability for long sequences to be found in database decreases.

1.4) The best match is "Chain A, Crystal structure of DNA polymerase sliding clamp from Bacillus subtilis" (accession number, 4TR6_A). The E-value is 0 (zero).

1.5) BLASTn compares the querry nucleotide sequence with nucleotide database while BLASTx compares querry nucleotide sequence with protein database. The results obtained from BLASTn are nucleotide sequences while results from BLASTx are protein sequences.

Related Questions

Navigate

• Browse (All)
• Browse P
• Subjects

Integrity-first tutoring: explanations and feedback only — we do not complete graded work. Learn more.