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Pairwise sequence comparison



Answers

  1. How does the dot-plot of the sequence above look like and why?

    Parallell diagonals appear as the sequence contains internal repeats.

  2. Obtain the Swissprot entries of the yeast hexokinase A
    and yeast hexokinase B proteins (see above) and create one fasta-file
    which contains both sequences.
    After having downloaded and compiled ReadSeq, the commandline to obtain the Fasta-File looks as follows:
    	readseq -f8 -p hxka_yeast hxkb_yeast > hxk_yeast.fasta
    

    And here is the content of the resulting file hxk_yeast.fasta:
    >HXKA_YEAST     STANDARD;      PRT;   485 AA., 485 bases, 8BF84D98 checksum.
    MVHLGPKKPQARKGSMADVPKELMDEIHQLEDMFTVDSETLRKVVKHFID
    ELNKGLTKKGGNIPMIPGWVMEFPTGKESGNYLAIDLGGTNLRVVLVKLS
    GNHTFDTTQSKYKLPHDMRTTKHQEELWSFIADSLKDFMVEQELLNTKDT
    LPLGFTFSYPASQNKINEGILQRWTKGFDIPNVEGHDVVPLLQNEISKRE
    LPIEIVALINDTVGTLIASYYTDPETKMGVIFGTGVNGAFYDVVSDIEKL
    EGKLADDIPSNSPMAINCEYGSFDNEHLVLPRTKYDVAVDEQSPRPGQQA
    FEKMTSGYYLGELLRLVLLELNEKGLMLKDQDLSKLKQPYIMDTSYPARI
    EDDPFENLEDTDDIFQKDFGVKTTLPERKLIRRLCELIGTRAARLAVCGI
    AAICQKRGYKTGHIAADGSVYNKYPGFKEAAAKGLRDIYGWTGDASKDPI
    TIVPAEDGSGAGAAVIAALSEKRIAEGKSLGIIGA
    >HXKB_YEAST     STANDARD;      PRT;   486 AA., 486 bases, B05F4DF9 checksum.
    MVHLGPKKPQARKGSMADVPKELMQQIENFEKIFTVPTETLQAVTKHFIS
    ELEKGLSKKGGNIPMIPGWVMDFPTGKESGDFLAIDLGGTNLRVVLVKLG
    GDRTFDTTQSKYRLPDAMRTTQNPDELWEFIADSLKAFIDEQFPQGISEP
    IPLGFTFSFPASQNKINEGILQRWTKGFDIPNIENHDVVPMLQKQITKRN
    IPIEVVALINDTTGTLVASYYTDPETKMGVIFGTGVNGAYYDVCSDIEKL
    QGKLSDDIPPSAPMAINCEYGSFDNEHVVLPRTKYDITIDEESPRPGQQT
    FEKMSSGYYLGEILRLALMDMYKQGFIFKNQDLSKFDKPFVMDTSYPARI
    EEDPFENLEDTDDLFQNEFGINTTVQERKLIRRLSELIGARAARLSVCGI
    AAICQKRGYKTGHIAADGSVYNRYPGFKEKAANALKDIYGWTQTSLDDYP
    IKIVPAEDGSGAGAAVIAALAQKRIAEGKSVGIIGA
    


  3. Align the yeast hexokinase A and yeast hexokinase B protein.
    (hint: use LALIGN which is found at Swissprot -> Proteomics tools)
    here is the output of LAlign:
    
    
    ALIGN calculates a global alignment of two sequences
     version 2.0uPlease cite: Myers and Miller, CABIOS (1989) 4:11-17
    hxka_yeast                                          485 aa vs.
    hxkb_yeast                                          486 aa
    scoring matrix: BLOSUM50, gap penalties: -14/-4
    77.4% identity;         Global alignment score: 2596
    
                   10        20        30        40        50        60
    /tmp/w MVHLGPKKPQARKGSMADVPKELMDEIHQLEDMFTVDSETLRKVVKHFIDELNKGLTKKG
           ::::::::::::::::::::::::..:...: .::: .:::. :.::::.::.:::.:::
    hxkb_y MVHLGPKKPQARKGSMADVPKELMQQIENFEKIFTVPTETLQAVTKHFISELEKGLSKKG
                   10        20        30        40        50        60
    
                   70        80        90       100       110       120
    /tmp/w GNIPMIPGWVMEFPTGKESGNYLAIDLGGTNLRVVLVKLSGNHTFDTTQSKYKLPHDMRT
           :::::::::::.::::::::..:::::::::::::::::.:..:::::::::.::  :::
    hxkb_y GNIPMIPGWVMDFPTGKESGDFLAIDLGGTNLRVVLVKLGGDRTFDTTQSKYRLPDAMRT
                   70        80        90       100       110       120
    
                  130       140       150       160       170       180
    /tmp/w TKHQEELWSFIADSLKDFMVEQELLNTKDTLPLGFTFSYPASQNKINEGILQRWTKGFDI
           :.. .::: ::::::: :. ::   . .. .:::::::.:::::::::::::::::::::
    hxkb_y TQNPDELWEFIADSLKAFIDEQFPQGISEPIPLGFTFSFPASQNKINEGILQRWTKGFDI
                  130       140       150       160       170       180
    
                  190       200       210       220       230       240
    /tmp/w PNVEGHDVVPLLQNEISKRELPIEIVALINDTVGTLIASYYTDPETKMGVIFGTGVNGAF
           ::.:.:::::.::..:.::..:::.:::::::.:::.::::::::::::::::::::::.
    hxkb_y PNIENHDVVPMLQKQITKRNIPIEVVALINDTTGTLVASYYTDPETKMGVIFGTGVNGAY
                  190       200       210       220       230       240
    
                  250       260       270       280       290       300
    /tmp/w YDVVSDIEKLEGKLADDIPSNSPMAINCEYGSFDNEHLVLPRTKYDVAVDEQSPRPGQQA
           ::: ::::::.:::.:::: ..:::::::::::::::.::::::::...::.:::::::.
    hxkb_y YDVCSDIEKLQGKLSDDIPPSAPMAINCEYGSFDNEHVVLPRTKYDITIDEESPRPGQQT
                  250       260       270       280       290       300
    
                  310       320       330       340       350       360
    /tmp/w FEKMTSGYYLGELLRLVLLELNEKGLMLKDQDLSKLKQPYIMDTSYPARIEDDPFENLED
           ::::.:::::::.:::.:... ..:...:.:::::. .:..::::::::::.::::::::
    hxkb_y FEKMSSGYYLGEILRLALMDMYKQGFIFKNQDLSKFDKPFVMDTSYPARIEEDPFENLED
                  310       320       330       340       350       360
    
                  370       380       390       400       410       420
    /tmp/w TDDIFQKDFGVKTTLPERKLIRRLCELIGTRAARLAVCGIAAICQKRGYKTGHIAADGSV
           :::.::..::..::. :::::::: ::::.:::::.::::::::::::::::::::::::
    hxkb_y TDDLFQNEFGINTTVQERKLIRRLSELIGARAARLSVCGIAAICQKRGYKTGHIAADGSV
                  370       380       390       400       410       420
    
                  430       440        450       460       470         
    /tmp/w YNKYPGFKEAAAKGLRDIYGWTGDASKD-PITIVPAEDGSGAGAAVIAALSEKRIAEGKS
           ::.:::::: ::..:.::::::  .  : :: ::::::::::::::::::..::::::::
    hxkb_y YNRYPGFKEKAANALKDIYGWTQTSLDDYPIKIVPAEDGSGAGAAVIAALAQKRIAEGKS
                  430       440       450       460       470       480
    
         480     
    /tmp/w LGIIGA
           .:::::
    hxkb_y VGIIGA
                 
    



    Comments are very welcome.
    luz@molgen.mpg.de