ClustalOmega:AligntwoormoreDNAorProteinSequencesStep1.Internetsearch“clustalomega”Step2.Orclickthislink:https://www.ebi.ac.uk/Tools/msa/clustalo/
Step3.You’llgetthispage:
Step4.Findsomesequencedatatoalign.Hereare3DNAsequencesinFASTAformatfromhttp://kelleybioinfo.org/algorithms/data/DAli2.txt
(The“Sequencefiles”linkontheBasicspagehasmoreinformationonFASTA.)
Step5.SelectDNAbecausetheseareDNAsequences,thenCopyandPastethedataintotheinputwindow.
>NucSeq1 ATGAACGACGAAACACAATTTACAAATAAGGCCAACGAAATTATCCGTTTGGCCCAGAAATTGGCTCAGGATCACAGACATGCTCAGTTACAACCAATTCACTTACTTGCTGCATTTGTTGAGCCAAACGAGGATGGTTC >NucSeq2 ATGGCTGATTATCCTTTTACTGACAAAGCCGCAAAGACATTGTCTGATGCGTACTCAATTGCACAATCTTATGGTCATTCACAATTAACCCCTATTCACATTGCTGCTGCTCTTTTGTCCGACAGTGACAGTAACGGTAC >NucSeq3 ATGAACGACGAAACGAAGTTTACGAACAAAGCTCTCGATATCATCACCATTGCACAGAAACTAGCACAGGACCACCAGCATTCGACGCTGGTGCCTCTACACGTGCTTGCAGCGTTCGTAGAGACACCTGCTGATGGTAG
Step6.ScrollDowntothebottomofthepageandclicktheSubmitbutton.
Step7.Thenwait….
Step8.Interpretingtheoutput.
Afterwaitingabit,theoutputwillappearinthebrowserlikethis:
Linkstodata,output,phylogeny.Downloadtoatextfile.
TheClustalformatin“interleaved”:thesealignmentsshow60alignmentpositionsforallsequences,thengotothenext60untilthereisnomorealignment.
Thesequencealignment:
Aasterisk“*”indicatesallthesequenceshavethesamenucleotide.Fullyconserved.
ClustalOmegaOptions
Clickinghere…
…willallowyoutochangealignmentsettings.
Mostimportantformostpeopleishowtochangeoutputformats.
Aligning Protein Sequences
Step1.SettoProtein(default).Step2.PasteinData(orchoosefile).Step3. Submit.
Step.4Waitforalignment
Meaningofsymbolsinproteinalignment:
*(Asterix) positionswithasingle,fullyconservedresidue.:(colon) positionswithconservationbetweenaminoacidgroupsofsimilarproperties..(period) positionswithconservationbetweenaminoacidgroupsofweaklysimilarproperties.
