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Pairwise Sequence Alignment Practice Manual

Use different tools to find true reading frames, compare sequences, and perform local/global alignments in bioinformatics practice.

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Pairwise Sequence Alignment Practice Manual

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  1. Pairwise sequence alignment (practice)

  2. Manual Work: Write down the amino acid sequences derived from all six possible reading frames of: >seq1 ACTGTCGC

  3. Open the following website http://biotools.umassmed.edu/cgi-bin/biobin/transeq Choose all frames Remove X

  4. Translate all possible reading frames of the following sequence TATGTCTCTCACCAACAAGAACGTCGTTTTCGTGGCCGGTCTGGGCGGCATTGGCCTGGAC ACCAGCCGGGAGTTGGTCAAGCGTAATCTGAAGAACCTGGTCATCCTGGATCGCATTGAC AATCCGGCTGCCATTGCCGAACTGAAGGCAATCAATCCCAAGGTGACCATCACCTTCTAT CCCTACGATGTGACTGTGCCCGTCGCTGAGACCACCAAGCTCCTGAAGACCATCTTTGCC CAGGTGAAGACAATCGATGTCCTGATCAACGGTGCTGGCATCCTGGACGATCATCAGATC GAGCGCACCATTGCCGTTAACTACACGGGCCTGGTCAACACCACCACAGCCATTCTGGAC TTCTGGGACAAGCGCAAGGGCGGCCCAGGCGGCATCATTTGCAACATTGGCTCCGTCACC GGTTTCAATGCCATCTACCAGGTGCCCGTTTACTCCGGCTCCAAGGCGGCGGTGGTTAAC TTTACCTCCTCCCTGGCGAAACTGGCTCCCATTACTGGTGTCACTGCTTACACTGTCAAT CCTGGCATCACCAGGACCACTCTGGTCCACAAATTCAACTCGTGGCTGGATGTGGAGCCC CGTGTGGCGGAGAAGCTGCTCGAGCATCCCACCCAGACCTCTCAGCAGTGCGCCGAGAAC TTTGTGAAGGCCATTGAGCTGAACAAGAACGGTGCCATCTGGAAGTTGGATTTGGGCACC TTGGAGCCCATCACATGGACCCAGCACTGGGACTCGGGCATCTAA Which reading frame(s) is(are) likely to be the true reading frame(s)?

  5. DOT-PLOT Give the coordinates of the boxes to be filled? A T C G G C A T A T C G G C A G Window size :5 Stringency: 5 Window size :5 Stringency: 2 A T C G G T A T A T C G G T A T A T C G G C A G A T C G G C A G

  6. Nucleic Acid Dot Plots (http://www.vivo.colostate.edu/molkit/dnadot/) Copy DNA sequences Compare Horse (NM_001164018) and Chicken (NM_001081704) hemoglobin Window size must be an odd number Number of mismatches allowed

  7. Use the Dotplot to compare chicken ovomucoid (NM_001112662) to itself GCACCGGCAGCCGCCTGCAGAGCCGGGCAGTACCTCACCATGGCCATGGCAGGCGTCTTCGTGCTGTTCT CTTTCGTGCTTTGTGGCTTCCTCCCAGATGCTGCCTTTGGGGCTGAGGTGGACTGCAGTAGGTTTCCCAA CGCTACAGACAAGGAAGGCAAAGATGTATTGGTTTGCAACAAGGACCTCCGCCCCATCTGTGGTACCGAT GGAGTCACTTACACCAACGATTGCTTGCTGTGTGCCTACAGCATAGAATTTGGAACCAATATCAGCAAAG AGCACGATGGAGAATGCAAGGAAACTGTTCCTATGAACTGCAGTAGTTATGCCAACACGACAAGCGAGGA CGGAAAAGTGATGGTCCTCTGCAACAGGGCCTTCAACCCCGTCTGTGGTACTGATGGAGTCACCTACGAC AATGAGTGTCTGCTGTGTGCCCACAAAGTAGAGCAGGGGGCCAGCGTTGACAAGAGGCATGATGGTGGAT GTAGGAAGGAACTTGCTGCTGTTGACTGCAGCGAGTACCCTAAGCCTGACTGCACGGCAGAAGACAGACC TCTCTGTGGCTCCGACAACAAAACATATGGCAACAAGTGCAACTTCTGCAATGCAGTCGTGGAAAGCAAC GGGACTCTCACTTTAAGCCATTTTGGAAAATGCTGAATATCAGAGCTGAGAGAATTCACCACAGGATCCC CACTGGCGAATCCCAGCGAGAGGTCTCACCTCGGTTCATCTCGCACTCTGGGGAGCTCAGCTCACTCCCG ATTTTCTTTCTCAATAAACTAAATCAGCAACAAAAAAAAAA

  8. What do these parallel lines represent?

  9. LALIGN - finds multiple matching subsegments in two sequences Part of the FASTA package of sequence analysis program. Lalign - compares two protein or DNA sequences for local or global similarity and shows the local sequence alignments. http://www.ch.embnet.org/software/LALIGN_form.html

  10. Choose method default matrix Set scoring matrix and gap penalties Paste your sequence

  11. Openhttp://www.ch.embnet.org/software/LALIGN_form.html Use the sequences below and perform a global alignment with 5 “Opening gap penalty” and 0 “Extending gap penalty”. >seq1 GCGACTGTTCCTATGAACTGCAGTAGTTATGCCAACACGACAAGCGAGGACGGAAAAGTGAGTCTGTGGTACTGATGGAGTCACCTACGACGCGAGGACGCCAGGTG >seq2 GCGAGGACGGAAAAGTG

  12. GLOBAL DOESN’T ALWAYS WORK. GLOBAL

  13. SOLUTION: LOCAL

  14. Write down the amino acid sequences derived from all six possible reading frames of: >seq1 ACTGTCGC >seqRC GCGACAGT Forward: >_1 TV >_2 LS >_3 CR Reverse >_1 AT >_2 RQ >_3 DS

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