Exercise
Perform a multiple alignment of the LDH-A protein sequences with Clustal Omega. You can change the order of the input sequences to see if there are any differences in the output. You can also remove the bacterial sequences from the input before running the alignment to see if there are any differences in the output.
There are two output files produced during the alignment process, the guide tree (XX.dnd) and the alignment file (XX.aln). Both files appear at the same time when the run is finished, but which of these files were actually created first by the program?
Sequences
Bacillus| MKNNGGARVVVIGAGFVGASYVFALMNQGIADEIVLIDANESKAIGDAMDFNHGKVFAPKPVDIWHGDYDDCRDADLVVICAGANQKPGETRLDLVDKNIAIFRSIVESVMASGFQGLFLVATNPVDILTYATWKFSGLPHERVIGSGTILDTARFRFLLGEYFSVAPQNVHAYIIGEHGDTELPVWSQAYIGVMPIRKLVESKGEEAQKDLERIFVNVRDAAYQIIEKKGATYYGIAMGLARVTRAILHNENAILTVSAYLDGLYGERDVYIGVPAVINRNGIREVIEIELNDDEKNRFHHSAATLKSVLARAFTR
Mouse_B| MATLKDQLIVNLLKEEQAPQNKITVVGVGAVGMACAISILMKDLADELALVDVMEDKLKGEMMDLQHGSLFLKTPKIVSSKDYCVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFIIPNIVKYSPHCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHALSCHGWVLGEHGDSSVPVWSGVNVAGVSLKSLNPELGTDADKEQWKEVHKQVVDSAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPISTMIKGLYGINEDVFLSVPCILGQNGISDVVKVTLTPEEEARLKKSADTLWGIQKELQF
Shark_A| MATVQQKLITPVSQERSDASRNKVTVVGVGQVGMACAVSILLRELTDEIALVDVLEDKLKGEMMDLLHGSLFLKTPKIMANKDYGITANSRVVVVTAGARQQEGESRLNLVQRNVNIFKFIIPQIVKYSPNCTIIVVSNPVDILTYVTWKISGFPKNRVIGSGCNLDSARFRYLMAEKLGLHPSSCHGWVLGEHGDSSVPVWSGVNVAGVGLQQLNPDIGTAQDKENWKDVHKMVVESAYEVIKLKGYTNWAIGLSVAELTESMVKNLKRVHPVSTMVKGMYGIENEVFLSLPCVLSADGLIDVINQMLKDDEVAQLRKSAETLWNIQKELKDL
Pig_B| MATLKDQLIHNLLKEEHVPHNKITVVGVGAVGMACAISILMKELADEIALVDVMEDKLKGEMMDLQHGSLFLRTPKIVSGKDYNVTANSRLVVITAGARQQEGESRLNLVQRNVNIFKFIIPNIVKYSPNCKLLVVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHPLSCHGWILGEHGDSSVPVWSGVNVAGVSLKNLHPELGTDADKEHWKAVHKQVVDSAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPISTMIKGLYGIKEDVFLSVPCILGQNGISDVVKVTLTPEEEAHLKKSADTLWGIQKELQF
Human_A| MATLKEKLIAPVAEEEATVPNNKITVVGVGQVGMACAISILGKSLADELALVDVLEDKLKGEMMDLQHGSLFLQTPKIVADKDYSVTANSKIVVVTAGVRQQEGESRLNLVQRNVNVFKFIIPQIVKYSPDCIIIVVSNPVDILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMAEKLGIHPSSCHGWILGEHGDSSVAVWSGVNVAGVSLQELNPEMGTDNDSENWKEVHKMVVESAYEVIKLKGYTNWAIGLSVADLIESMLKNLSRIHPVSTMVKGMYGIENEVFLSLPCILNARGLTSVINQKLKDDEVAQLKKSADTLWDIQKDLKDL
Chicken_B| MSLKDHLIHNVHKEEHAHAHNKISVVGVGAVGMACAISILMKDLADELTLVDVVEDKLKGEMLDLQHGSLFLKTPKIISGKDYSVTAHSKLVIVTAGARQQEGESRLNLVQRNVNIFKFIIPNVVKYSPDCKLLIVSNPVDILTYVAWKISGFPKHRVIGSGCNLDSARFRHLMGERLGIHPLSCHGWIVGEHGDSSVPVWSGVNVAGVSLKALHPDMGTDADKEHWKEVHKQVVDSAYEVIKLKGYTSWAIGLSVADLAETIMKNLRRVHPISTAVKGMHGIKDDVFLSVPCVLGSSGITDVVKMILKPDEEEKIKKSADTLWGIQKELQF
Mouse_A| MATLKEKLIASVADDEAAVPNNKITVVGVGQVGMACAISILGKSLADELALVDVLEDKLKGEMMDLQHGSLFLQTPKIVADKDYSVTANSKIVVVTAGVRQQEGESRLNLVQRNVNVFKFIIPQIVKYSPDCTIIVVSNPVDILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMAEKLGIHPSSCHGWILGEHGDSSVAVWSGVNVAGVSLQELNPEMGTDNDSENWKEVHKMVVDSAYEVIKLKGYTNWAIGLSVADLIESMLKNLSRIHPVSTMVKGMYGIENEVFLSLPCILNARGLTSVINQKLKDDEVAQLRKSADTLWDIQKDLKDL
Rabbit_B| MAALKDQLIHNLLKEEHVPQNKITVVGVGAVGMACAISILMKDLADELALVDVMEDKLKGEMMDLQHGSLFLRTPKIVSGKDYSVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFIIPNVVKYSPHCKLLVVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHALSCHGWILGEHGDSSVPVWSGMNVAGVSLKTLHPELGTDADKEQWKQVHKQVVDSAYEVIKLKGYTTWAIGLSVADLAESIMKNLRRVHPISTMLKGLYGIKEDVFLSVPCVLGQNGISDVVKVTLTSEEEAHLKKSADTLWGIQKELQF
Rat_A| MATLKEKLIAPVADDETAVPNNKITVVGVGQVGMACAISILGKSLADELALVDVLEDKLKGEMMDLQHGSLFLQTPKIVADKDYSVTANSKIVVVTAGVRQQEGESRLNLVQRNVNVFKFIIPQIVKYSPDCTIIVVSNPVDILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMAEKLGIHPSSCHGWILGEHGDSSVAVWSGVNVAGVSLQELNPEMGTDNDSENWKEVHKMVVDSAYEVIKLKGYTNWAIGLSVADLIESMLKNLSRIHPVSTMVKGMYGIENEVFLSLPCILNARGLTSVINQKLKDDEVAQLRKSADTLWDIQKDLKDL
Pig_A| MATLKEKLIAPVAEEETTIPNNKITVVGVGQVGMACAISILGKSLTDELALVDVLEDKLKGEMMDLQHGSLFLQTPKIVADKDYSVTANSKIVVVTAGVRQQEGESRLNLVQRNVNVFKFIIPQIVKYSPDCIIIVVSNPVDILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMAEKLGVHPSSCHGWILGEHGDSSVAVWSGVNVAGVSLQELNPEMGTDNDSENWKEVHKMVVESAYEVIKLKGYTNWAIGLSVADLIESMLKNLSRIHPVSTMVQGMYGIENEVFLSLPCVLNARGLTSVINQKLKDDEVAQLKNSADTLWGIQKDLKDL
Rabbit_A| GKFIIPQIVKYSPNCIIIVVSNPVDILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMAEKLGIHPSSCHGWILGEHGDSRLAVWSGVNVAGVSLQELNPEMGTDNDSENWKEVHKMVVESAYEVIKLKGYTNWAIGLSVADLIESMLKNLSRIHPVSTMVRGMYGIESEVFLSLPCILNARGLTSVINQKLKDDEVAQLKKSADTLWDIQKDLKDL
Barley_B| AGDASSGFFRAVADGCPITHTSCSAPHRRLTKVSVIGAGNVGMAIAQTILTQNLADEIALVDALPDKLRGEALDLQHAAAFLPRVRIVSGTDAAVTKNSDLIVVTAGARQIPGETRLNLLQRNVALYRKIVPPVAEHSPDALLLVVSNPVDVLTYVAWKLSGFPASRVIGSGTNLDSSRFRFLVAEHLDVSAQDVQAYMVGEHGDSSVAIWSSISVGGMPALKSLRDSHRSFDEAALEGIRRAVVGGAYEVIGLKGYTSWAIGYSVASLATSLLRDQRRVHPVSVLAAGFHGISDGHEVFLSLPARLGRAGVLGVAEMDLTEAEAAQLRRSAKTLWENCQLLGL
Human_B| MATLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKGEMMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFIIPNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIKGLYGIKDDVFLSVPCILGQNGISDLVKVTLTSEEEARLKKSADTLWGIQKELQF
Thermotoga| MKIGIVGLGRVGSSTAFALLMKGFAREMVLIDVDKKRAEGDALDLIHGTPFTRRANIYAGDYADLKGSDVVIVAAGVPQKPGETRLQLLGRNARVMKEIARNVSKYAPDSIVIVVTNPVDVLTYFFLKESGMDPRKVFGSGTVLDTARLRTLIAQHCGFSPRSVHVYVIGEHGDSEVPVWSGAMIGGIPLQNMCQICQKCDSKILENFAEKTKRAAYEIIERKGATHYAIALAVADIVESIFFDEKRVLTLSVYLEDYLGVKDLCISVPVTLGKHGVERILELNLNEEELEAFRKSASILKNAINEITAEENKHQNTSG
Chicken_A| MATLKEKLITPVAAGSTVPSNKITVVGVGQVGMACAISILGKGLCDELALVDVLEDKLKGEMMDLQHGSLFLQTHKIVADKDYAVTANSKIVVVTAGVRQQEGESRLNLVQRNVNVFKFIIPQIVKYSPNCTILVVSNPVDILTYVTWKLSGLPKHRVIGSGCNLDTARFRYLMAERLGIHPTSCHGWILGEHGDSSVAVWSGVNVAGVSLQELNPAMGTDKDSENWKEVHKQVVESAYEVIRLKGYTNWAIGLSVAELCETMLKNLYRVHSVSTLVKGTYGIENDVFLSLPCVLSASGLTSVINQKLKDDEVAQLKKSADTLWSIQKDLKDL
Rat_B| MAALKDQLIVNLLKEEQVPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKGEMMDLQHGSLFLKTPKIVSSKDYSVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFIIPNVVKYSPQCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHPLSCHGWVLGEHGDSSVPVWSGVNVAGVSLKSLNPQLGTDADKEQWKDVHKQVVDSAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPISTMIKGLYGIKEDVFLSVPCILGQNGISDVVKVTLTPDEEARLKKSADTLWGIQKELQF
Shark_B| MATLKDKLIGHLATSQEPRSYNKITVVGVGAVGMACAISILMKDLADEVALVDVMEDKLKGEMMDLQHGSLFLHTAKIVSGKDYSVSAGSKLVVITAGARQQEGESRLNLVQRNVNIFKFIIPDIVKHSPDCIILVVSNPVDVLTYVAWKLSGLPMHRIIGSGCNLDSARFRYLMGERLGVHSSSCHGWVIGEHGDSSVPVWSGMNVAGVSLKELHPELGTDKDKENWKKLHKDVVDSAYEVIKLKGYTSWAIGLSVADLAETIMKNLCRVHPVSTMVKDFYGIKNDVFLSLPCVLDNHGISNIVKMKLKPDEEQQLQKSATTLWDIQKDLKF
Barley_A| MHKASSLSELGFDAGGASSGFFRPVADGCPATPTSSAVPHRRLTKISVIGAGNVGMAIAQTILTQNLADEIALVDALPDKLRGEALDLQHAAAFLPRVRISGTDAAVTKNSDLVIVTAGARQIPGETRLNLLQRNVALYRKIVPPVAEHSPDALLLVVSNPVDVLTYVAWKLSGFPASRVIGSGTNLDSSRFRFLIAEHLDVNAQDVQAYMVGEHGDSSVAIWSSISVGGMPAFKSLRDSHRSFDEAALEGIRRAVVGGAYEVIGLKGYTSWAIGYSVASLAASLLRDQRRVHPVSVLASGFHGISDGHEVFLSLPARLGRGGILGVAEMDLTEAEAAQLRRSAKTLWENCQLLDL
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Since you took the effort and marked the actual question in bold people will be happy to solve your HW.
I hope so, I've tried, but can't quite get the correct answer.
I think my teacher is hinting to that the alignment occurs in two steps, one before the phylogenetic tree and one after, so the tree file is created first? I've been strugling and want to give her a good answer this time.
All the answers are in: http://www.ncbi.nlm.nih.gov/pubmed/3243435
Thanks! I was searching for papers, strange that I did not find that one.. :/
"want to give her a good answer this time"
Is this the reason to study? To please your teacher? Or should your teacher teach you what you don't understand? She's getting paid for it, you know...
Unfortunately this is the crapiest, most uninspiring course I've ever taken and I've lost all interest for it. The teachers aren't doing anything to help us understand.. Not in my opinion at least.. Now I'm stuck with it and trying just to pass the course or I don't get my bachelor degree.. They don't even give lectures, just pre-written instructions which are very poor.