Week4-Lab-BLAST Assignment

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Bioinformatics: Tools for Genomic Analysis Week 4: Searching similar sequencing using BLAST Total Points: 30 Exercise 1. (i) What is the accession number for this record? NP_000015 (ii) How many amino acids long is this protein? 413 AA (iii) List top three hits with their respective E values? (3 points) IGNORE predicted or hypothetical results. hypothetical protein JTE90_000975 [Oedothorax gibbosus] : 6e-74 beta-2 adrenergic receptor [Parasteatoda tepidariorum] : 2e-73 octopamine receptor beta-2R [Parasteatoda tepidariorum] : 3e-71 Receptor, partial [Dermatophagoides pteronyssinus] :5e-70 (iv) What is the accession number for this record? NM_000024 (v) What is the range of nucleotides that span the coding region? 222..1463 (v) How many databases matches have an E value less than 0.001 for blastn search? 1 Match (vi) Of the two searches you performed- which one is more informative and Why? Blastn was found to have a lesser level of sequence identity compared to Blastp. Whereas in Blastp the search is more sensitive than blastp.

Exercise 2: Is a hippopotamus more closely related to a pig or to a whale? (4 points) To answer this question, first find the protein sequence of hemoglobin from each of those three organisms. Note down their accession number below: (1.5 points) Hippopotamus: P19016 Full=Hemoglobin subunit beta P19015 Full=Hemoglobin subunit alpha Pig: NP_001138313 hemoglobin subunit beta [Sus Scrofa] XP_020942625 hemoglobin subunit alpha Whale: XP_004279312 hemoglobin subunit beta [Orcinus orca] XP_004270432 hemoglobin subunit alpha Next, perform pairwise sequence alignments using BLASTp and option to align two sequences. (1.5 points) Hemoglobin subunit alpha [Hippopotamus] VS hemoglobin subunit alpha [Pig]- E-value: 1e-92 Percentage Identity: 88.65% Hemoglobin subunit beta [Hippopotamus] VS hemoglobin subunit beta [Pig]- E-value: 5e-97 Percentage Identity: 86.99% Hemoglobin subunit alpha [Hippopotamus] VS hemoglobin subunit alpha [Orcinus orca]- E-value: 8e-88 Percentage Identity: 80.85% Hemoglobin subunit beta [Hippopotamus] VS hemoglobin subunit beta [Orcinus orca]- E-value: 2e-89 Percentage Identity: 86.99% Hemoglobin subunit alpha [Pig ] Vs Hemoglobin subunit alpha [Hippopotamus] E-value: 1e-83 Percentage Identity : 78.17% hemoglobin subunit beta [Pig] Vs Hemoglobin subunit beta [Hippopotamus] E-value: 2e-84 Percentage Identity : 81.63% Now, analyze and answer the above-mentioned question and give your rationale below: (1 point) Hemoglobin subunit beta [Hippopotamus] is the most closely related to hemoglobin subunit beta [Pig] because it has the least e-value among all of them. E-value: 5e-97

Exercise 3 Based on the annotation of these sequence records, identify what gene was used in their analysis (1 point). 16S ribosomal RNA gene is used for the analysis For each BLASTN search, survey the results graphic, table, and alignments to assign each unknown sequence (aka accession numbers provided) to an organism. AY187314 - Holophaga sp. WY42 96.76% AY187315 - Streptococcus pneumonia strain 21.2T 98.77% AY187316 - Glacihabitans sp. strain KG3R40 98.68% AY187317 - Sphingopyxis sp. HP2 98.90% AY187318 - Spbingorhabdys lacys strain IMCC1753 99.67% AY187325 - Bradyrhizobium elkanii strain STB147 98.47% AY187326 - Pedomicrobium americanum strain IFAM G-1381- 98.24% AY187330 - Uncultured Legionella sp. clone 89-98.33% AY187332 - Candidatus Legionella jeonil 97.19% AY187838 - Acinetobacter sp. PG6-MRL 99.13%

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Exercise 4. Advanced BLAST What is the current version of this protein? How long is it? (2 points) NP_032244 142 aa However, he forgot the accession number for the corresponding mRNA. Can you find it out? How long is the mRNA? (2 points) NM_008218 569 bp What is the accession number of the corresponding DNA of this protein? (Hint: it is a genomic DNA, find it via Gene) What is the region (start and end position) of the corresponding DNA of your protein locating on the genomic DNA? (2 points) NC_000077 at 11 A4 (32233672...32234486) 815bp Now let’s run blastx. Use the mRNA and DNA you found from above questions as query respectively and compare the results. Which one offers better alignments? Can you speculate the reason why? (2 points) Protein and mRNA offer a better alignment because its percent identity is 100% and E-value:2e-105 which is better compared to Protein and DNA. Now turn to tblastn. Use the protein as query. What kind of molecules does it hit most? Does it make sense? (2 points) Hemoglobin molecules are hit the most. Yes, it makes sense because this protein encodes for the hemoglobin subunit alpha of Mus musculus

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