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Choice of the best matrix and parameters for GDH sequences alignment |
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The alignments are made using : ClustalW at EBI (Cambridge) Reference : Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994) "CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice" Nucleic Acids Res. 22, p 4673 - 4680
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Finally, "eye" inspection allows to choose the Gonnet matrix although the highest score is obtained with the Id matrix. 1. Id matrix : Gapopen = 1 - Other default values : SCORE = 26720 gi|15240793|ref|NP_196361.1| ILG-LDSKI----ERSLMI-PFREIKVECTIPKDDGTLVSYIGFRVQHDN 60 gi|15004984|dbj|BAB62170.1| ILG-LDSKI----EKSLMI-PFREIKVECTIPKDDGTLVSYVGFRVQHDN 60 gi|28269441|gb|AAO37984.1| LLG-LDSKL----EKSLLI-PFREIKVECTIPKDDGTLASYVGFRVQHDN 60 gi|7431768|pir||T16982 LLG-LDSKL----EQCLLI-PFREIKVECTIPKDDGSLATFIGFRVQHDN 60 gi|15054452|dbj|BAB62312.1| -LAVLD--LPPAMEK-IVITPQREMTVELIINRDDGKPESFMGYRVQHDN 94 gi|15054450|dbj|BAB62311.1| -LAVLD--LPPAMEK-IVITPQREMTVELIINRDDGKPESFMGYRVQHDN 94 *. ** : *: ::* * **:.** * :***. :::*:****** 2. GONNET matrix : Gapopen = 1 - Other default values : SCORE = 26243 gi|15240793|ref|NP_196361.1| ILGLDSKIERSLMIPFREIKVECTIPKDDGTLVSYIGFRVQHDNARGPMK 66 gi|15004984|dbj|BAB62170.1| ILGLDSKIEKSLMIPFREIKVECTIPKDDGTLVSYVGFRVQHDNARGPMK 66 gi|28269441|gb|AAO37984.1| LLGLDSKLEKSLLIPFREIKVECTIPKDDGTLASYVGFRVQHDNARGPMK 66 gi|7431768|pir||T16982 LLGLDSKLEQCLLIPFREIKVECTIPKDDGSLATFIGFRVQHDNARGPMK 66 gi|15054452|dbj|BAB62312.1| VLDLPPAMEKIVITPQREMTVELIINRDDGKPESFMGYRVQHDNARGPFK 100 gi|15054450|dbj|BAB62311.1| VLDLPPAMEKIVITPQREMTVELIINRDDGKPESFMGYRVQHDNARGPFK 100 :*.* . :*: :: * **:.** * :***. :::*:**********:* |
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