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Multiple sequence alignment correction using constraints
December 2010
Gu2010
In this work, we present a framework to impose constraints over the sequences, and we show how it is possible to apply alignments based on different criteria just setting constraint among the amino acids. This framework can be applied not only for the improving the alignment and detection of coevolved regions, but also to any desired constraints that may be used to express functional or structural relations among the amino acids in multiple sequences. We show also that after we fix this misalignments, using the constraints based techniques, the coevolved sites increase they correlation and in general the new alignment is closer to the correct alignment than the MSA alignment. Finally, we show possible future research lines with the objective of overcome some drawbacks detected during this work.
M. Sc. dissertation
Luciano Guasco
Ludwig Krippahl
FCT/UNL, (EMCL)
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Luciano Guasco, Multiple sequence alignment correction using constraints, Ludwig Krippahl (superv.), FCT/UNL, (EMCL), December 2010.
<b>Luciano Guasco</b>, <u>Multiple sequence alignment correction using constraints</u>, <a href="/people/members/view.php?code=195d68ea5904b58472fd8c8aedcae233" class="supervisor">Ludwig Krippahl</a> (superv.), FCT/UNL, (EMCL), December 2010.
@mastersthesis {Gu2010, author = {Luciano Guasco}, title = {Multiple sequence alignment correction using constraints}, school = {FCT/UNL, (EMCL)}, note = {Ludwig Krippahl (superv.); }, abstract = {In this work, we present a framework to impose constraints over the sequences, and we show how it is possible to apply alignments based on different criteria just setting constraint among the amino acids. This framework can be applied not only for the improving the alignment and detection of coevolved regions, but also to any desired constraints that may be used to express functional or structural relations among the amino acids in multiple sequences. We show also that after we fix this misalignments, using the constraints based techniques, the coevolved sites increase they correlation and in general the new alignment is closer to the correct alignment than the MSA alignment. Finally, we show possible future research lines with the objective of overcome some drawbacks detected during this work.}, month = {December}, year = {2010}, }
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