Question

QUESTIONS 1) Do a BLASTP search using RBP4 (NP_006735), restricting the output to Arthropoda (Insects). How many databases matches have an Evalue less than 0.01 in this search? (10 points) 2) Next, do a BLASTN search using the RBP4 nucleotide sequence (NM_006744). For this query, select only the nucleotides corresponding to the coding region of the DNA. (To do this visit the NCBI Nucleotide page, follow the link to the coding sequence [CDS), then choose the FASTA format.) How many databases matches have an Evalue less than 0.01 in this search? (10 points) Which search is more informative? How many databases matches have an Evalue less than 0.01 in each search? For the toolbar, press ALT+F10 (PC) or ALT+FN+F10 (Mac). TTTT Paragraph Arial 3 (12) EE. T- %DOQ T T2S - 1. For the E value of 0.01, it is shown that there are matches for all human protein with mosses plant. 2, the query result for masses after using blast search shows the Click Save and Submit to save and submit. Click Save All Answers to sate all answers. Save All Answers

Answer 1

I will mention the correct answer along with the procedure of its retrieval.

1) Upon doing a BLASTP search of NP_006735 and restricting the output to just Arthropoda, a total of 599 database matches were obtained. Then the results were filtered with respect to E-value. After applying the filter, 225 databases were found to have E-value less than 0.01 . So the correct answer should be 225.

2) Firstly NM_006744 was searched on NCBI under Nucloetide parameter. Then its Coding Sequences (CDS) were retrieved by clicking on CDS and then downloading its FASTA file. After that, the FASTA sequence was searched in BLASTN. A total of 367 database matches were obtained.Then the results were filtered with respect to E-value. After applying the filter, all databases were found to have E-value less than 0.01 . So the correct answer should be 367.

Out of these two, BLASTN will be more informative than BLASTP. This is because of the fact that an amino acid can be coded by multiple codons (called codon degeneracy). Hence upon comparing nucleotide sequences, we canaccurately estimate the relative closeness of the search query. On the other hand, if we compare protein sequences, then multiple codons can code for a single amino acid. So the comparison won't be that much accurate relative to BLASTN.

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