Bioinformatics for DNA Sequence Analysis.pdf - Index of

26 Egan et al.trees (termed guide trees) are screened for the presence of charactersdiagnostic of orthologs using the CAOS algorithm (3) andthe identification of unknown queries is made through comparisonof the guide tree diagnostics and the query sequence. In this waytrees are not required to be constructed each time a new query’sorthology is identified.Table 2.1Description of homology approaches showing the methods used to establishhomology and focus of applicationApproach and steps Description of step Purpose or method Applied todePinna (dP)1. Primary homology Establish charactercodingInterpret anatomy (similarto characterassignment)Anatomy2. SecondaryhomologyPhylogenetic analysisDiscover shared andderivedness to establishhomology (identicalto step 3 in BS)Brower Schawaroch (BS)1. TopographicalsimilaritySequence alignment New aspect not in dP Molecularsequences2. Characterassignment3. PhylogeneticanalysisAssess charactertransformationsDiscover sharedand derivednessSimple for DNA andproteins to establishhomology(Identical to step 2 in dP)Gene family homology (GFH)1. TopographicalsimilarityBLAST/BLATEstablishes hypothesis ofgene family inclusionGene presenceabsence studies;gene familystudies2. CharacterassignmentAlignment of geneEstablishes characterassignment forsequences3. PhylogeneticanalysisBecause target nowis organismalphylogenetic analysisaccomplishes genehomologyassessmentEstablishes gene familyhomologies bydemonstrating sharedderived origin for familymembers