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.