Gene Classification Based on Amino Acid Motifs and Residues The DLX (distal-less) Test Case 英文参考文献.docVIP

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Gene Classification Based on Amino Acid Motifs and Residues The DLX (distal-less) Test Case 英文参考文献.doc

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Gene Classification Based on Amino Acid Motifs and Residues The DLX (distal-less) Test Case 英文参考文献

GeneClassificationBasedonAminoAcidMotifsand Residues:TheDLX(distal-less)TestCase NunoA.Fonseca1,2,CristinaP.Vieira1,JorgeVieira1* 1InstitutodeBiologiaMoleculareCelular(IBMC);UniversityofPorto,Porto,Portugal,2CRACS-INESCPorto,UniversidadedoPorto,Porto,Portugal Abstract Background:Comparativestudiesusinghundredsofsequencescangiveadetailedpictureoftheevolutionofagivengene family. Nevertheless, retrieving only the sequences of interest from public databases can be difficult, in particular, when working with highly divergent sequences. The difficulty increases substantially when one wants to include in the study sequencesfrommany(orlesswellstudied)specieswhosegenomesarenon-annotatedorincompletelyannotated. Methodology/Principal Findings: In this work we evaluate the usefulness of different approaches of gene retrieval and classification, using the distal-less (DLX) gene family as atest case. Furthermore, we evaluate whether the use of a large numberofgenesequencesfromawiderangeofanimalspecies,theuseofmultiplealternativealignments,andtheuseof aminoacidsalignedwithhighconfidenceonly,isenoughtorecovertheacceptedDLXevolutionaryhistory. Conclusions/Significance: The canonical DLX homeobox gene sequence here derived, together with the characteristic aminoacidvariantshereidentifiedintheDLXhomeodomainregion,canbeusedtoretrieveandclassifyDLXgenesina simpleandefficientway.Aprogramismadeavailablethatallowstheeasyretrievalofsyntenyinformationthatcanbeused to classify genesequences. Maximumlikelihood trees using hundreds of sequences can be used for gene identification. Nevertheless,fortheDLXcase,theproposedDLXevolutionaryisnotrecoveredevenwhenmultiplealignmentalgorithms areused. Citation: Fonseca NA,VieiraCP,VieiraJ(2009) GeneClassificationBasedonAminoAcidMotifsandResidues: The DLX(distal-less)TestCase.PLoSONE 4(6): e5748.doi:10.1371/journal.pone.0005748 Editor:RobertDeSalle,AmericanMuseumofNaturalHistory,UnitedStatesofAmerica ReceivedSeptember25,2008;AcceptedMay4,2009;Pub