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  • Identity: Identity: - : Similarity: 97/175 (55.4%) Gaps: 13/175 (7.4%)

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    Lam Phạm
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    The document reports the results of performing local and global sequence alignments of the mouse hypoxanthine phosphoribosyl transferase (HPRT) protein and the same enzyme from E. coli. A local alignment found 36.0% identity and 55.4% similarity, with 7.4% gaps. A global alignment found lower identity (28.6%) but more gaps (23.2%) than the local alignment. Changing the gap penalty in the local alignment resulted in a similar identity (36.5%) but more gaps (21.5%).

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    ass3.question1

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    The document reports the results of performing local and global sequence alignments of the mouse hypoxanthine phosphoribosyl transferase (HPRT) protein and the same enzyme from E. coli. A local alignment found 36.0% identity and 55.4% similarity, with 7.4% gaps. A global alignment found lower identity (28.6%) but more gaps (23.2%) than the local alignment. Changing the gap penalty in the local alignment resulted in a similar identity (36.5%) but more gaps (21.5%).

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    31 views2 pages

    Identity: Identity: - : Similarity: 97/175 (55.4%) Gaps: 13/175 (7.4%)

    Uploaded by

    Lam Phạm
    The document reports the results of performing local and global sequence alignments of the mouse hypoxanthine phosphoribosyl transferase (HPRT) protein and the same enzyme from E. coli. A local alignment found 36.0% identity and 55.4% similarity, with 7.4% gaps. A global alignment found lower identity (28.6%) but more gaps (23.2%) than the local alignment. Changing the gap penalty in the local alignment resulted in a similar identity (36.5%) but more gaps (21.5%).

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    of 2

    Question 1: In the NCBI database, retrieve the protein sequences for mouse hypoxanthine

    phosphoribosyl transferase (HPRT) (NP_038584) and the same enzyme from E. coli (WP_103280448) in
    FASTA format.

    a. Perform a local alignment of the two sequences using Water in EMBL-EBI EMBOSS
    (https://www.ebi.ac.uk/Tools/psa/). Report identity, similarity & gaps
    -Identity: identity: 63/175 (36.0%)
    -Similarity: 97/175 (55.4%)
    -Gaps: 13/175 ( 7.4%)

    b. Perform a global alignment of the two sequences using Needle in EMBL-EBI EMBOSS
    (https://www.ebi.ac.uk/Tools/psa/). Compare the results with those from the local alignment.

    - Global alignment:

    - Compare:
    Local aligniment Global alignment
    Identity 63/175 (36.0%) 64/224 (28.6%)
    Similarity 97/175 (55.4%) 102/224 (45.5%)
    Gaps 13/175 ( 7.4%) 52/224 (23.2%)

    c. Change the default gap penalty from“10/0.5” to “5/0.1”. Run the local alignment and compare the
    results with previous local alignment.
    - Results after changing the default gap penalty from “10 / 0.5” to “5 / 0.1” of lobal alignment

    - Compare:

    Previous local alignment Local alignment afterwards


    Identity 63/175 (36.0%) 73/200 (36.5%)
    Similary 97/175 (55.4%) 105/200 (52.5%)
    Gaps 13/175 ( 7.4%) 43/200 (21.5) %

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