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•Howtousethistool
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Using ClustalW for Sequence Alignment and Phylogenetic Analysis, Slides of Proteomics
Clustalw is a tool for aligning nucleotide and protein sequences for comparison. It calculates the best match for selected sequences and lines them up to identify similarities and differences. The tool can also be used to produce a phylogenetic tree. How to use clustalw, including how to input sequences and adjust various parameters for optimal alignment and analysis.
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2011/2012
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Introduction
Howtousethistool
Phylograms.relationshipscanbeseenviaviewingCladograms orsimilaritiesanddifferencescanbeseen.Evolutionarysequences,andlinesthemupsothattheidentities,attemptstocalculatethebestmatchfortheselectednucleotideandproteinsequencesforcomparison.ItClustalW isaprogram,whichallowsyoutoalign
Allowyoutofind areasofsimilarityanddissimilarity
patternswithinthenucleotidesequence.
Itcanalsobeusedto produceaphylogenetictree.
asinputforthemultiplesequencealignment.UniProtKB/SwissProt)canbeuploadedandusedanyformat(GCG,FASTA,EMBL,PIR,NBRForAfilecontainingthreeormorevalidsequencesin
Wordprocessorfilesmayyieldunpredictable presentinthefiles.resultsashidden/controlcharactersmaybe
ItisbesttosavefileswiththeUnixformatoption toavoidhiddenWindowscharacters.
Thereisalimitof500sequencesor1MBofdata.
ornucleotide(DNA/RNA).Indicatesifthesequencestoalignareprotein Defaultvalueis:Protein[protein] Type Abbreviation Protein protein DNA dna
guidetree.pairwise alignmentsusedtogeneratetheThealignmentmethodusedtoperformthe Defaultvalueis:slow OutputFormat Description Abbreviation slow Slow, but accurate slow fast approximateFast,but fast
alignment.comparisonmatrixseriesusedtoscoreSlowpairwise alignmentproteinsequence Defaultvalueis:Gonnet [gonnet] Only) Matrix(Protein Description Abbreviation BLOSUM blosum PAM pam Gonnet gonnet ID id
residueinagap.Slowpairwise alignmentscoreforthefirst Defaultvalueis:
additionalresidueinagap.Slowpairwise alignmentscoreforeach Defaultvalueis:0.
increaseforsensitivity.joiningwordmatches.Decreaseforspeed;Fastpairwise alignmentwindowsizefor Defaultvalueis:
Fastpairwise alignmentscoretypetooutput. Defaultvalueis:percent Order Description Abbreviation percent percent absolute absolute
gapcreated.Fastpairwise alignmentgappenaltyforeach Defaultvalueis: