Bioinformatics for DNA Sequence Analysis.pdf - Index of

Multiple Alignment of DNA Sequences with MAFFT 41ac>Sequence1nnnnnnattccggttgatcctgccggaggccactgctatcggggtccgactaagccatgcgagtcaaggggctcccttcggggagcaccggcgcacggctcagtaacacgtggctaacctaccctcgggtgggggataacctcgggaaactgaggctaatcccccataggggaggaggtctggaatgatccctccccgaaaggcgtaagctgcccgaggatggggctgcggcggattaggagtgaggccctgtccgcaagggcagggtcgaacttgggttcagcgaggggggcgaagtcgtaacaaggtagccgtaggggaactgcggctggatcacctccnnnnn>Sequence2nnnnnnactccggttgatcctgccggaggccaccgctatcggggtccgactaagccatgcaagtcgagggccgcccggcaatgggggcggcccggcggacggctcagtaacacgtgggtaacctaccctcgggacggggataaccccggcgaaagtggggctaatccccgataggcggggcggcctggaacggtcctccgccgaaagggcccgggcccatgccgcccgggtccgcccgaggatgggcctgcggccgattaggtagttggcggggtaacggcccgccaagccgataatcggtacgggcggtgagagccggagcccggagacggggactga>Sequence3agtggggaatcttggacaatgggggaaaccctgatccagcgacgccgcgtgcgggacgaagcccttcggggtgtaaaccgctgtggcgggggaagaataaggtagggaggaaatgccctatgtcggatgtgaaatcccacggctcaaccgtggggctgcatccgaaactaccaggcttggtctCLUSTAL W (1.83) multiple sequence alignmentSequence1 --NNNNNNATTCCGGTTGATCCTGCCGGAGGCCACTGCTATCGGGGTCCGACTAAGCCATSequence2 --NNNNNNACTCCGGTTGATCCTGCCGGAGGCCACCGCTATCGGGGTCCGACTAAGCCATSequence3 AGTGGGGAATCTTGGACAAT------GGGGGAAACCCTGATCCAG---CGACGCCGC-GT* ** ** ** ** ** *** * **** ** *b>Sequence1nnnnnnattccggttgatcctgccggaggccactgctatcggggtccgactaagccatgcgagtcaaggggctccc----ttcggggagcaccggcgcacggctcagtaacacgtggctaacctaccctcgggtgggggataacctcgg-gaaactgaggctaatcccccataggggaggaggtctggaatgatccctccccgaaagg-----------------cgtaagctgcccgaggatggggctgcggcggattaggagtgaggccctgtccgcaagggcagggtcgaacttgggttcagcgaggggggcgaagtcgtaacaaggtagccgtag---gggaactgcggctggatcacctccnnnnn>Sequence2nnnnnnactccggttgatcctgccggaggccaccgctatcggggtccgactaagccatgcaagtcgagggccgcccggcaatgggggcggcccggcggacggctcagtaacacgtgggtaacctaccctcgggacggggataaccccggcgaaagtggggctaatccccgataggcggggcggcctggaacggtcctccgccgaaagggcccgggcccatgccgcccgggtccgcccgaggatgggcctgcggccgattaggtagttggcggggt-----aacggcccgccaagccgataatcggtacgggcggtgag-------------agccggagcccggagacggggactga-------------->Sequence3ag--------tggggaatcttg--gacaatgggggaaaccctgatccagcgacgccgcgtgcgggacgaagccctt----cggggtgtaaaccgctgtg-----------------------------gcgggggaagaataaggtagg--------gaggaaatgccctatgtcggatgtgaaatcccacg-----------------------------------------gctcaaccgtggggctgcatccga--aactaccaggcttggtct----------------------------------------------------------------------------------------------Sequence1 GCGAGTCAAGGGGCTCCCTTC----GGGGAGCACCGGCGCACGGCTCAGTAACACGTGGCSequence2 GCAAGTCGAGGGCCGCCCGGCAATGGGGGCGGCCCGGCGGACGGCTCAGTAACACGTGGGSequence3 GCGGGACGAAGCCCTTCGGGGTGT-AAACCGCTGTGGCGGG-GGAAGAATAAGGTAGGGA** * * * * * * * **** ** * *** **Sequence1 TAACCTACCCT---CGGGTGGGGGATAACCTCGG-GAAACTGAGGCTAATCCCCCATAGGSequence2 TAACCTACCCT---CGGGACGGGGATAACCCCGGCGAAAGTGGGGCTAATCCCCGATAGGSequence3 GGAAATGCCCTATGTCGGATGTGAAATCCCACGGCTCAACCGTGGGG------CTGCATC* * **** ** * * * ** *** ** * ** * *Sequence1 GGAGGAGGTCTGGAATGATCCCTCCCCGAAAGGCGTAAGCTGCCCGAGGATGGGGCTGCGSequence2 CGGGGCGGCCTGGAACGGTCCTCCGCCGAAAGGGCCCGG--GCCCATG---CCGCCCGGGSequence3 CGAAACTACCAGGCTTGGTCT---------------------------------------* * ** * **Sequence1 GCGGATTAGGAGTGAGGCCCTGTCCGCAAGGGCAGGGTCGAACTTGGGTTCAGCGAGGGGSequence2 TCCGCCCGAGGATGGGCCTGCGGCCGATTAGGTA--GTTGG---CGGGGTAA---CGGCCSequence3 ------------------------------------------------------------Sequence1 GGCGAAGTCGTAACAAGGTAGCCGTAG-GGGAACTGCGGCTGGATCACCTCCNNNNNSequence2 CGCCAAGCCGATAATCGGTACGGGCGGTGAGAGCCGGAGCCCGGAGACGGGGACTGASequence3 ---------------------------------------------------------Fig. 3.1. (a) Multiple unaligned sequences in the FASTA format. (b) Multiple alignment in the FASTA format. (c) Multiple alignment in the CLUSTAL format.