Go to http://blast.ncbi.nlm.nih.gov/Blast.cgi and follow...

Question

Go to http://blast.ncbi.nlm.nih.gov/Blast.cgi and follow the links to nucleotide blast. Type in the sequence below; it is broken up into codons to make it easier to copy.

5' ATG TTC GTC AAT CAG CAC CTT TGT GGT TCT CAC CTC GTT GAA GCTTTG TAC CTT GTT TGC GGT GAA CGT GGT TTC TTC TAC ACT CCT AAG ACT TAA 3'

As you will note on the BLAST page, there are several options for tailoring your query to obtain the most relevant information. Some are related to which sequences to search in the database. For example, the search can be limited taxonomically (e.g., restricted to mammals) or by the type of sequences in the database (e.g., cDNA or genomic). For our search, we will use the broadest database, the 'Nucleotide collection (nr/nt).' This is the nonredundant (nr) database of all nucleotide data (nt) in GenBank and can be selected in the 'Database' dialogue box. Other parameters can also be adjusted to make the search more or less sensitive to mismatches or gaps. For our purposes, we will use the default setting, which is automatically presented. Press 'BLAST' to search. What can you say about the DNA sequence?

Accepted Answer

Hey everyone. Let's take a look at this question together. Blast, which stands for basic local alignment. Search tool is a sequence comparison tool that is used to identify homologous sequences by comparing a query sequence to a database of known sequences. What is the minimum length of the words used by blast? When comparing protein sequences? Is it 7 to 8 amino acids, 9 to 10 amino acids, 3 to 4 amino acids or 10 to 12 amino acids. Let's work this problem out together to try to figure out how many amino acids is the minimum length of the words that are used by blast when comparing protein sequences. So since blast is a search tool, we want to determine what a good minimum length of the words used by blast could be when comparing those protein sequences. And we use the term words loosely because we are talking about those amino acids. And since we are looking for comparisons among other sequences, we want to determine what the amount of words would be to equal the most matches among that search for blast, which we know that searching for short words would equal the most matches among all of the sequences in the blast database. Since shorter words are more likely to match across multiple sequences, making it easier to identify those homologous sequences. So looking at our answer choices, we see that answer choice C has 3 to 4, which is the lowest number of amino acid, any answer choices. And so it is the shortest amount of words or amino acids that blast could use to receive the most matches in its search. So answer choice C 3 to 4 amino acids is the minimum length of the words used by a blast. When comparing protein sequences, I hope you found this video to be helpful. Thank you and goodbye.

Key Concepts

DNA Sequence

BLAST (Basic Local Alignment Search Tool)

Nucleotide Database

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