Pairwise sequence alignment practice 1 Manual Work Write

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Pairwise sequence alignment (practice) 1

Pairwise sequence alignment (practice) 1

Manual Work: Write down the amino acid sequences derived from all six possible reading

Manual Work: Write down the amino acid sequences derived from all six possible reading frames of: >seq 1 ACTGTCGC 2

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

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

Translate all possible reading frames of the following sequence TATGTCTCTCACCAACAAGAACGTCGTTTTCGTGGCCGGTCTGGGCGGCATTGGCCTGGAC ACCAGCCGGGAGTTGGTCAAGCGTAATCTGAAGAACCTGGTCATCCTGGATCGCATTGAC AATCCGGCTGCCATTGCCGAACTGAAGGCAATCCCAAGGTGACCATCACCTTCTAT CCCTACGATGTGACTGTGCCCGTCGCTGAGACCACCAAGCTCCTGAAGACCATCTTTGCC CAGGTGAAGACAATCGATGTCCTGATCAACGGTGCTGGCATCCTGGACGATCATCAGATC

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

DOT-PLOT Give the coordinates of the boxes to be filled? A T C G

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

Nucleic Acid Dot Plots (http: //www. vivo. colostate. edu/molkit/dnadot/) Compare Horse (NM_001164018) and Chicken

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

Use the Dotplot to compare chicken ovomucoid (NM_001112662) to itself GCACCGGCAGCCGCCTGCAGAGCCGGGCAGTACCTCACCATGGCAGGCGTCTTCGTGCTGTTCT CTTTCGTGCTTTGTGGCTTCCTCCCAGATGCTGCCTTTGGGGCTGAGGTGGACTGCAGTAGGTTTCCCAA CGCTACAGACAAGGCAAAGATGTATTGGTTTGCAACAAGGACCTCCGCCCCATCTGTGGTACCGAT GGAGTCACTTACACCAACGATTGCTGTGTGCCTACAGCATAGAATTTGGAACCAATATCAGCAAAG

Use the Dotplot to compare chicken ovomucoid (NM_001112662) to itself GCACCGGCAGCCGCCTGCAGAGCCGGGCAGTACCTCACCATGGCAGGCGTCTTCGTGCTGTTCT CTTTCGTGCTTTGTGGCTTCCTCCCAGATGCTGCCTTTGGGGCTGAGGTGGACTGCAGTAGGTTTCCCAA CGCTACAGACAAGGCAAAGATGTATTGGTTTGCAACAAGGACCTCCGCCCCATCTGTGGTACCGAT GGAGTCACTTACACCAACGATTGCTGTGTGCCTACAGCATAGAATTTGGAACCAATATCAGCAAAG AGCACGATGGAGAATGCAAGGAAACTGTTCCTATGAACTGCAGTAGTTATGCCAACACGACAAGCGAGGA CGGAAAAGTGATGGTCCTCTGCAACAGGGCCTTCAACCCCGTCTGTGGTACTGATGGAGTCACCTACGAC AATGAGTGTCTGCTGTGTGCCCACAAAGTAGAGCAGGGGGCCAGCGTTGACAAGAGGCATGATGGTGGAT GTAGGAACTTGCTGCTGTTGACTGCAGCGAGTACCCTAAGCCTGACTGCACGGCAGAAGACC TCTCTGTGGCTCCGACAACAAAACATATGGCAACAAGTGCAACTTCTGCAATGCAGTCGTGGAAAGCAAC GGGACTCTCACTTTAAGCCATTTTGGAAAATGCTGAATATCAGAGCTGAGAGAATTCACCACAGGATCCC CACTGGCGAATCCCAGCGAGAGGTCTCACCTCGGTTCATCTCGCACTCTGGGGAGCTCACTCCCG ATTTTCTCAATAAACTAAATCAGCAACAAAAA

What do these parallel lines represent?

What do these parallel lines represent?

LALIGN - finds multiple matching subsegments in two sequences Part of the FASTA package

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 11

Choose method default matrix Set scoring matrix and gap penalties Paste your sequence 12

Choose method default matrix Set scoring matrix and gap penalties Paste your sequence 12

Open http: //www. ch. embnet. org/software/LALIGN_form. html Use the sequences below and perform a

Open http: //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”. >seq 1 GCGACTGTTCCTATGAACTGCAGTAGTTATGCCAACACG ACAAGCGAGGACGGAAAAGTGAGTCTGTGGTACTGATGG AGTCACCTACGACGCGAGGACGCCAGGTG >seq 2 GCGAGGACGGAAAAGTG 13

GLOBAL DOESN’T ALWAYS WORK. GLOBAL 14

GLOBAL DOESN’T ALWAYS WORK. GLOBAL 14

SOLUTION: LOCAL 15

SOLUTION: LOCAL 15

Write down the amino acid sequences derived from all six possible reading frames of:

Write down the amino acid sequences derived from all six possible reading frames of: >seq 1 ACTGTCGC >seq. RC GCGACAGT Forward: >_1 TV >_2 LS >_3 CR Reverse >_1 AT >_2 RQ >_3 DS 16

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