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1、DNAsequencing:?T?heDNASequenceQuality-?Phred??-?providesbasecalling,chromatogramdisplayandhighqualitysequenceregionevaluationandpresentationforuptofivesequencessimultaneously.??Sequenceassembly-youdon'tneedyourowncontigassemblyprogramwhenyoucanuse:??EGassember?-alignsandmergessequencefragmentsres
2、ultingfromshotgunsequencingorgenetranscripts(EST)fragmentsinordertoreconstructtheoriginalsegmentorgene(Reference:?A.Masoudi-Nejadetal.2006.Nucl.AcidsRes.?34:?W459-462).?CAP3?(PBIL,France),??CAPESTAssembler(IstitutoFIRCdiOncologiaMolecolare,Italy)?-Maximumsequencelengthforeachsequenceis30kb?-Maxim
3、umnumberofsequences10kb??Divide-and-ConquerMultipleSequenceAlignment?(UniversitatBielefeld,Germany)?Sequencingerrors-ifyourDNAsequencedoesn'tmatchtheexpectedproteinsequenceyoucancheckforerrorsat?ERR_WISE?or?Wise2:?IntelligentalgorithmsforDNAsearches(EBI,UnitedKingdom)or??SEQERR??-?DetectionofFram
4、eshiftErrorsinCodingRegions?In-silico.com?(Dr.JosebaBikandi&co-workers,FacultyofPharmacy,intheUniversityoftheBasqueCountry)?-?allows?insilico?experimentsincludingtheoreticalPCRamplification,AFLP-PCR,restrictionanalysisandpulsedfieldgelelectrophoresis[PFGE]withbacterial&archaelgenomesfoundinthepub
5、licdatabase.?Genomecomparisons:??GeneOrder2.0?(D.Seto,?Bioinformatics&ComputationalBiology,GeorgeMasonUniv.,U.S.A.)??isidealforcomparingsmallGenBankgenomes(upto0.25Mb),while?GeneOrder3.0?extendsthelimitstoapprox.2.0Mb.EachgenefromtheQuerysequenceiscomparedtoallofthegenesfromtheReferencedatabaseus
6、ingBLASTP.Therearetwodisplayformats:graphicalandtabular.Currentlythegraphisanappletandmustbesavedasa"SCREENSHOT".?CoreGenes??(D.Seto,?Bioinformatics&ComputationalBiology,GeorgeMasonUniv.,U.S.A.)?isdesignedtoanalyzetwotofivegenomessimultaneously,generatingatableofrelatedgenes-orthologsandputativeo
7、rthologs.TheseentriesarelinkedtotheirGenBankdata.?Ithasalimitof0.35Mb,whilethenewerversion?CoreGenes2.0?extendsthelimitto?approx.2.0Mb.IfyourdataisnotpresentinGenBankuse?thissite.?CoreGenes3?(D.Seto&P.Mahadevan,Bioinfo
