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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
