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    W9-SIO1003 Practical 4-Questions

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    1. The document provides instructions for a bioinformatics practical assignment involving BLAST sequence analysis. 2. Students are given unknown DNA/RNA/protein sequences and must use BLAST to identify sequences, find similarities to sequences in databases, and answer questions to learn about the sequences and organisms. 3. The assignment involves analyzing single sequences and sets of sequences to determine species, common features, and the purpose of the experimental work that generated the sequences.

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    W9-SIO1003 Practical 4-Questions

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    23005852
    86 views6 pages
    1. The document provides instructions for a bioinformatics practical assignment involving BLAST sequence analysis. 2. Students are given unknown DNA/RNA/protein sequences and must use BLAST to identify sequences, find similarities to sequences in databases, and answer questions to learn about the sequences and organisms. 3. The assignment involves analyzing single sequences and sets of sequences to determine species, common features, and the purpose of the experimental work that generated the sequences.

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    1. The document provides instructions for a bioinformatics practical assignment involving BLAST sequence analysis. 2. Students are given unknown DNA/RNA/protein sequences and must use BLAST to identify sequences, find similarities to sequences in databases, and answer questions to learn about the sequences and organisms. 3. The assignment involves analyzing single sequences and sets of sequences to determine species, common features, and the purpose of the experimental work that generated the sequences.

    Copyright:

    © All Rights Reserved
    Download as DOCX, PDF, TXT or read online from Scribd
    Download as docx, pdf, or txt
    86 views6 pages

    W9-SIO1003 Practical 4-Questions

    Uploaded by

    23005852
    1. The document provides instructions for a bioinformatics practical assignment involving BLAST sequence analysis. 2. Students are given unknown DNA/RNA/protein sequences and must use BLAST to identify sequences, find similarities to sequences in databases, and answer questions to learn about the sequences and organisms. 3. The assignment involves analyzing single sequences and sets of sequences to determine species, common features, and the purpose of the experimental work that generated the sequences.

    Copyright:

    © All Rights Reserved
    Download as DOCX, PDF, TXT or read online from Scribd
    Download as docx, pdf, or txt
    of 6

    SIO1003 Bioinformatics Concepts

    Semester 1, Session 2023/2024

    Practical 4: BLAST (20 marks)

    Name: NUR AIN BASHIRAH BINTI ZAHRUL HAKIM


    Matrix No: 23005852
    Group: OCC 3

    Instruction:
    1. Two questions are given. Each question carries 10 marks. Answer all questions.
    2. Please send in your answers either in .doc/.docx/.pdf format via Spectrum-UM with
    a filename as follows: SIO1003_ID_FIRSTNAME_W9_P4
    3. Please also be reminded that plagiarism is an academic offense. If you are found to
    have plagiarized your colleague’s work, you will be penalized with 0 mark.
    4. Submission Deadline: Next Tuesday 11.59 pm

    Brief description about BLAST:


    BLAST programs from NCBI are powerful sequence alignment tools widely used in the
    analyses of biological sequences. It is also used to look for similar sequences in a
    database.
    In this exercise you will be given some sequences (DNA or RNA or Protein) and you are
    required to do some search and analyses using NCBI BLAST services
    (blast.ncbi.nlm.nih.gov) to address some specific biological questions.
    The purpose of these exercises are to help you to familiarize yourself with the web
    interface and better understand the capability of different BLAST programs.
    Exercise 1: Finding an unknown gene.
    Your supervisor has conducted a PCR experiment and given you an unknown
    sequence for analysis. The sequence is as below:
    >Unknown_sequence_1
    AAATGAGTTAATAGAATCTTTACAAATAAGAATATACACTTCTGCTTAGGATGATAAT
    TGGAGGCAAGTGAATCCTGAGCGTGATTTGATAATGACCTAATAATGATGGGTTTT
    ATTTCCAGACTTCACTTCTAATGGTGATTATGGGAGAACTGGAGCCTTCAGAGGGT
    AAAATTAAGCACAGTGGAAGAATTTCATTCTGTTCTCAGTTTTCCTGGATTATGCCT
    GGCACCATTAAAGAAAATATCATCTTTGGTGTTTCCTATGATGAATATAGATACAGA
    AGCGTCATCAAAGCATGCCAACTAGAAGAGGTAAGAAACTATGTGAAAACTTTTTG
    ATTATGCATATGAACCCTTCACACTACCCAAATTATATATTTGGCTCCATATTCAATC
    GGTTAGTCTACATATATTTATGTTTCCTCTATGGGTAAGCTACTGTGAATGGATCAA
    TTAATAAAACACATGACCTATGCTTTAAGAAGCTTGCAAACACATGAA

    Guidelines to conduct sequence analysis


    1. Navigate to the main BLAST page ( https://blast.ncbi.nlm.nih.gov/Blast.cgi )
    2. Select the appropriate type of BLAST for your sequence
    3. Paste the first unknown sequence into the box
    (for this activity, you can ignore the search options)
    4. Click on the “BLAST” button and wait for the results.
    5. Once the results are displayed, notice there are three main headings:
    Graphic Summary, Descriptions, and Alignments (these may be expanded so you’ll
    have to scroll down).
    6. Use these results to answer the questions below.
    Questions:
    1. In the Descriptions section, look at the top result, which should be the result with
    the highest score. Write down information about the best match:

    a. Description
    (no need to write the whole thing)
    =Homo sapiens CF transmembrane conductance regulator (CFTR),
    RefSeqGene (LRG_663) on chromosome 7
    b. E value

    = 0.0
    c. Percent identity
    =503/503(100%)

    d. Query cover

    =100%

    2. Now scroll down to the Alignments heading. Look at the top result, which should
    be the same one. Look at the alignment between your query and the reference.
    Do you see any mismatches?
    = No mismatch.

    3. How can you judge whether this is a good match?


    = Because the query cover is 100%, the E value is 0.0, and the overall score is
    high.

    4. What is this gene? Google the name of the gene and write down something
    significant you learned about it.
    = CTFR gene
    This gene encodes a member of the ATP-binding cassette (ABC) transporter
    superfamily. The encoded protein functions as a chloride channel, making it
    unique among members of this protein family, and controls ion and water
    secretion and absorption in epithelial tissues. Channel activation is mediated by
    cycles of regulatory domain phosphorylation, ATP-binding by the nucleotide-
    binding domains, and ATP hydrolysis. Mutations in this gene cause cystic
    fibrosis, the most common lethal genetic disorder in populations of Northern
    European descent. The most frequently occurring mutation in cystic fibrosis,
    DeltaF508, results in impaired folding and trafficking of the encoded protein.
    Multiple pseudogenes have been identified in the human genome.
    Exercise 2: Investigating sets of sequences
    Assume that you have joined as a staff at a bioinformatics company after your
    undergraduate study. There, your supervisor is actively involved in research, and he
    has a number of sequences which he had obtained from experimental work –
    sequencing experiment. He has given three sets of sequences for you to analyze and
    obtain some information from them.
    The given sequences are as in the table below:

    >Sequence1a
    GTAATGTACATAACATTAATGTAATAAAGA

    >Sequence1b
    SET 1
    ATCACGAGCTTAATTACCATGCCGCGTGAAACCAGCAACC

    >Sequence1c
    ATGGACTAATGGCTAATCAGCCCATGCTCACACATA

    >Sequence2a
    TTTGGTTGTTCGACGACGGATGCAGAGCTCAGGGAAGTGGGGACGTGTTTTG
    GCTATCCT

    >Sequence2b
    GCGATGCATCAGGATGCATCCTCTGATCTTAGGGTGGTACGAGAAAAATTGA
    SET 2
    AGAATGTA

    >Sequence2c
    GCGGTTCCACAAGACCCTGAGGCGCCTGGTGCCTGACTCGGACGTCCGGTT
    CCTCCTCTC

    SET 3
    >Sequence3a
    TAACCTACGGGTGGCCGCAGTGGGGAATATTGCACAATGGACACAAGTCTGA
    TGCAGCGACGCCGCGTGGGGGATGAAGGCTTTCGGGTTGTAAACTCCTTTC
    AGTACAGAAGAAGCATTTTTGTGACGGTATGTGCAGAAGAAGCGCCGGCTAA
    CTACGTGCCAGCAGCCGCGGTAATACGTAGGGCGCGAGCGTTGTCCGGAAT
    TATTGGGCGTAAAGAGCTCGTAGGCGGTTTGTTGCGCCTGCTGTG

    >Sequence3b
    TGTCCTACGGGGGGCTGCAGTGAGGAATATTGGTCAATGGGCGAGAGCCTG
    AACCAGCCAAGTCGCGTGAAGGATGACTGTCTTATGGATTGTAAACTTCTTTT
    ATACGGGAATAACAAGAGTCACGTGTGGCTCCCTGCATGTACCGTATGAATA
    AGCATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGATGCGAGC
    GTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGC

    >Sequence3c
    GGCCTACGGGGGGCTGCAGTGGGTACGGGCAGACTAGAGTGTGGTAGGGG
    TAATTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACAC
    CGATGGCGAAGGCAGGTTACTGGGCCATTACTGACGCTGAGGAGCGAAAGC
    GTGGGTAGCGAACAGGATTAGATACCCTAGTAGTCT

    Guidelines to conduct sequence analysis.

    1. Navigate to the main BLAST page ( https://blast.ncbi.nlm.nih.gov/Blast.cgi )


    2. Select the appropriate type of BLAST for your sequence
    3. Paste the first set (set 1) sequences into the box and click BLAST button by leaving
    other parameters in default values.
    4. Once the results are displayed, notice at the three main headings: Graphic
    Summary, Descriptions, and Alignments.
    5. Use these results to answer the questions below.

    Questions: for each experimental set, answer these questions,


    1. Description
    2. Maximum score
    3. E-Value
    4. Sequence ID
    5. Query cover
    6. Query length
    7. Which organism do these sequences belong to?
    8. What do these sequences have in common?
    9. What is your best guess about the original purpose of this experiment?
    No Aspect Set 1 Set 2 Set 3
    1 Description Bos taurus Arabidopsis Trueperella
    mitochondrial thaliana pyogenes
    DNA, D-loop, genome strain TN2 16S
    complete assembly, ribosomal RNA
    sequence, chromosome: gene, partial
    haplotype: 4 sequence
    JSH35_1
    2 Maximum score 56.5 bits(30) 111 bits(60) 442 bits (239)
    3 E-value 4e-05 8e-21 2e-119
    4 Sequence ID LC314271.2 LR782545.1 MT269339.1
    5 Query cover 100% 100% 98%
    6 Query length 30 60 63
    7 Which organism do these Cattle Thale cress Bacteria
    sequences belong to
    8 What do these sequences  The genetic material of every organism is
    have in common? read by all of these sequences.
     They have high query coverage , meaning
    query coverage more than 98%
     The E-value of these sequences are
    significant , meaning the alignments are
    most probably correct
    9 What is your best guess To identify and analyze the unknown sequences to
    about the original purpose obtain information on species of the organism the
    of this experiment? sequences belongs to , by comparing with existing
    data in the databases.

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