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    Aamena Yusuf
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    The document discusses pairwise sequence alignment of retinol-binding protein (RBP) and β-lactoglobulin. It shows an alignment of the two proteins with some positions being identical or similar and other positions containing gaps. The alignment identifies internal gaps within the sequences as well as terminal gaps. Pairwise alignment is useful for identifying mutations that occurred during evolution and caused divergence between sequences, such as substitutions, insertions and deletions. Gaps in an alignment occur where a position is aligned with a null, and gap scores are usually negative to reflect the lower probability of indels.

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    The document discusses pairwise sequence alignment of retinol-binding protein (RBP) and β-lactoglobulin. It shows an alignment of the two proteins with some positions being identical or similar and other positions containing gaps. The alignment identifies internal gaps within the sequences as well as terminal gaps. Pairwise alignment is useful for identifying mutations that occurred during evolution and caused divergence between sequences, such as substitutions, insertions and deletions. Gaps in an alignment occur where a position is aligned with a null, and gap scores are usually negative to reflect the lower probability of indels.

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    8 views9 pages

    Lecture 4

    Uploaded by

    Aamena Yusuf
    The document discusses pairwise sequence alignment of retinol-binding protein (RBP) and β-lactoglobulin. It shows an alignment of the two proteins with some positions being identical or similar and other positions containing gaps. The alignment identifies internal gaps within the sequences as well as terminal gaps. Pairwise alignment is useful for identifying mutations that occurred during evolution and caused divergence between sequences, such as substitutions, insertions and deletions. Gaps in an alignment occur where a position is aligned with a null, and gap scores are usually negative to reflect the lower probability of indels.

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    © All Rights Reserved
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    of 9

    Unit No: 1: Pairwise Sequence Analysis

    Lecture No: 4
    Local Alignment, Global
    Alignment, Gap penalties
    Definitions

    Pairwise alignment
    The process of lining up two sequences to achieve maximal levels of identity
    (and conservation, in the case of amino acid sequences) for the purpose of
    assessing the degree of similarity and the possibility of homology

    Homology
    Similarity attributed to descent from a common ancestor.
    Two sequences are homologous if they share a common ancestory

    Identity & Similarity are quantities that describe the relatedness of sequences

    Similarity: attributed to descent from a common ancestor. The extent to which


    nucleotide or protein sequences are related. It is based upon identity plus
    conservation.

    Identity: The extent to which two sequences are invariant.

    2 Lecture 4 – Local Alignment, Global Alignment, Gap penalties


    Definitions

    Conservation
    Changes at a specific position of an amino acid or (less commonly, DNA)
    sequence that preserve the physico-chemical properties of the original residue

    Orthologs
    Homologous sequences in different species that arose from a common
    ancestral gene during speciation; may or may not be responsible
    for a similar function.

    Paralogs
    Homologous sequences within a single species that arose by gene duplication

    3 Lecture 4 – Local Alignment, Global Alignment, Gap penalties


    Pairwise alignment of retinol-binding protein and b-lactoglobulin

    1 MKWVWALLLLAAWAAAERDCRVSSFRVKENFDKARFSGTWYAMAKKDPEG 50 RBP
    . ||| | . |. . . | : .||||.:| :
    1 ...MKCLLLALALTCGAQALIVT..QTMKGLDIQKVAGTWYSLAMAASD. 44 lactoglobulin

    51 LFLQDNIVAEFSVDETGQMSATAKGRVR.LLNNWD..VCADMVGTFTDTE 97 RBP
    : | | | | :: | .| . || |: || |.
    45 ISLLDAQSAPLRV.YVEELKPTPEGDLEILLQKWENGECAQKKIIAEKTK 93 lactoglobulin

    98 DPAKFKMKYWGVASFLQKGNDDHWIVDTDYDTYAV...........QYSC 136 RBP


    || ||. | :.|||| | .
    Identity .|
    (bar)
    94 IPAVFKIDALNENKVL........VLDTDYKKYLLFCMENSAEPEQSLAC 135 lactoglobulin

    137 RLLNLDGTCADSYSFVFSRDPNGLPPEAQKIVRQRQ.EELCLARQYRLIV 185 RBP


    . | | | : || . | || |
    136 QCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLEEQCHI....... 178 lactoglobulin

    4 Lecture 4 – Local Alignment, Global Alignment, Gap penalties


    Pairwise alignment of retinol-binding protein and b-lactoglobulin

    1 MKWVWALLLLAAWAAAERDCRVSSFRVKENFDKARFSGTWYAMAKKDPEG 50 RBP
    . ||| | . |. . . | : .||||.:| :
    1 ...MKCLLLALALTCGAQALIVT..QTMKGLDIQKVAGTWYSLAMAASD. 44 lactoglobulin

    51 LFLQDNIVAEFSVDETGQMSATAKGRVR.LLNNWD..VCADMVGTFTDTE 97 RBP
    : | | | | :: | .| . || |: || |.
    45 ISLLDAQSAPLRV.YVEELKPTPEGDLEILLQKWENGECAQKKIIAEKTK 93 lactoglobulin

    98 DPAKFKMKYWGVASFLQKGNDDHWIVDTDYDTYAV...........QYSC 136 RBP


    || ||. Somewhat
    | :.|||| | . Very
    .|
    similar similar135 lactoglobulin
    94 IPAVFKIDALNENKVL........VLDTDYKKYLLFCMENSAEPEQSLAC
    (one dot) (two dots)
    137 RLLNLDGTCADSYSFVFSRDPNGLPPEAQKIVRQRQ.EELCLARQYRLIV 185 RBP
    . | | | : || . | || |
    136 QCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLEEQCHI....... 178 lactoglobulin

    5 Lecture 4 – Local Alignment, Global Alignment, Gap penalties


    Pairwise alignment of retinol-binding protein and b-lactoglobulin

    1 MKWVWALLLLAAWAAAERDCRVSSFRVKENFDKARFSGTWYAMAKKDPEG 50 RBP
    . ||| | . |. . . | : .||||.:| :
    1 ...MKCLLLALALTCGAQALIVT..QTMKGLDIQKVAGTWYSLAMAASD. 44 lactoglobulin

    51 LFLQDNIVAEFSVDETGQMSATAKGRVR.LLNNWD..VCADMVGTFTDTE 97 RBP
    : | | | | :: | .| . || |: || |.
    45 ISLLDAQSAPLRV.YVEELKPTPEGDLEILLQKWENGECAQKKIIAEKTK 93 lactoglobulin

    98 DPAKFKMKYWGVASFLQKGNDDHWIVDTDYDTYAV...........QYSC 136 RBP


    || ||. | :.|||| | . .|
    94 IPAVFKIDALNENKVL........VLDTDYKKYLLFCMENSAEPEQSLAC 135 lactoglobulin

    137 RLLNLDGTCADSYSFVFSRDPNGLPPEAQKIVRQRQ.EELCLARQYRLIV 185 RBP


    . | | | : || . | || |
    136 QCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLEEQCHI....... 178 lactoglobulin

    Internal Terminal
    gap gap
    6 Lecture 4 – Local Alignment, Global Alignment, Gap penalties
    GAPS

    Pairwise align is useful as a way to identify mutations occurred during


    evolution and have caused divergence.

    Common mutations are substitutions, insertions and deletions

    • Positions at which a letter is paired with a null are called gaps.

    • Gap scores are typically negative.

    • Since a single mutational event may cause the insertion or deletion of


    more than one residue, the presence of a gap is ascribed more
    significance than the length of the gap.

    • In BLAST, it is rarely necessary to change gap


    values from the default.

    7 Lecture 4 – Local Alignment, Global Alignment, Gap penalties


    Aligning Sequences….

    There are lots of possible alignments.

    Two sequences can always be aligned.

    Sequence alignments have to be scored.

    Often there is more than one solution with the same score.

    8 Lecture 4 – Local Alignment, Global Alignment, Gap penalties


    Thank You

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