The following is a hypothetical scenario NOT related to your Blast search. You sequenced a 16S rRNA DNA sequence from a newly discovered microbe. After you performed a BLAST search, you found the following data. 1. Identify = 96% 2. Query coverage = 100% Based on the above data, what can you conclude about the newly discovered organism. The organism belong to eukaryotic microbe The organism belong to already known species The data presented is not sufficient to deduct a conclusion It is novel species which has never been sequenced
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What does it mean if the closest matched organism that is returned from a BLAST search is less than a 97% match to an organism you are sequencing?
Sulav P.
The sequence alignments generated by BLAST provide the best alignment of the query sequence with sequences within the database. Scientists can use this large database to help to identify biological samples. The program DNA Barcoding for Life is focused on identifying biological diversity within ecosystems. Environmental DNA collection and analysis has been used to help identify species that exist in a location that may be difficult to physically spot or collect. Question 3. While DNA isolation and a BLAST search is a powerful manner in which to identify a specimen, there can be accurate sequences that do not match anything in the database. What are two possible explanations that you could use to explain the lack of a perfect match between your query sequence and the database?
Sana R.
Assume that you have just sequenced a small fragment of DNA that you had cloned. The nucleotide sequence of this segment of DNA is as follows. In an attempt to learn something about the identity or possible function of this DNA sequence, you decide to perform a BLAST (nucleotide blast) search on PubMed's Entrez web site (http://www.ncbi.nlm.nih.gov/entrez). Paste or type this sequence into the query sequence box. Run the search and examine the sequences most closely related to your query sequence. Are they coding sequences? What proteins do they encode? The first sequence listed is NM $079795.2 .$ Go to the Entrez "Search across databases" tool (click the box at the bottom of the Entrez home page), type or paste $\mathrm{NM}_{-} 079795.2$ in as the query, and click on Go. You will get results ("hits") in five databases: Nucleotide, Gene, HomoloGene, Probe, and UniGene. Examine the information in all five databases and see what you can learn about the function of your DNA or the protein that it encodes. What have you learned about your DNA sequence from these searches? Repeat the BLAST search with only half of your sequence as the query sequence. Do you still identify the same sequences in the databases? If you use one-fourth of your sequence as a query, do you still retrieve the same sequences? What is the shortest DNA sequence that you can use as a query and still identify the same sequences in the databanks?
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