Pairwise sequence alignment (practice)

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Pairwise sequence alignment (practice)
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Manual Work Write down the amino acid sequences
derived from all six possible reading frames
of gtseq1 ACTGTCGC
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• Open the following website
• http//biotools.umassmed.edu/cgi-bin/biobin/transe
  q

Choose all frames
Remove X
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Translate all possible reading frames of the
following sequence

• TATGTCTCTCACCAACAAGAACGTCGTTTTCGTGGCCGGTCTGGGCGGCA
  TTGGCCTGGAC
• ACCAGCCGGGAGTTGGTCAAGCGTAATCTGAAGAACCTGGTCATCCTGGA
  TCGCATTGAC
• AATCCGGCTGCCATTGCCGAACTGAAGGCAATCAATCCCAAGGTGACCAT
  CACCTTCTAT
• CCCTACGATGTGACTGTGCCCGTCGCTGAGACCACCAAGCTCCTGAAGAC
  CATCTTTGCC
• CAGGTGAAGACAATCGATGTCCTGATCAACGGTGCTGGCATCCTGGACGA
  TCATCAGATC
• GAGCGCACCATTGCCGTTAACTACACGGGCCTGGTCAACACCACCACAGC
  CATTCTGGAC
• TTCTGGGACAAGCGCAAGGGCGGCCCAGGCGGCATCATTTGCAACATTGG
  CTCCGTCACC
• GGTTTCAATGCCATCTACCAGGTGCCCGTTTACTCCGGCTCCAAGGCGGC
  GGTGGTTAAC
• TTTACCTCCTCCCTGGCGAAACTGGCTCCCATTACTGGTGTCACTGCTTA
  CACTGTCAAT
• CCTGGCATCACCAGGACCACTCTGGTCCACAAATTCAACTCGTGGCTGGA
  TGTGGAGCCC
• CGTGTGGCGGAGAAGCTGCTCGAGCATCCCACCCAGACCTCTCAGCAGTG
  CGCCGAGAAC
• TTTGTGAAGGCCATTGAGCTGAACAAGAACGGTGCCATCTGGAAGTTGGA
  TTTGGGCACC
• TTGGAGCCCATCACATGGACCCAGCACTGGGACTCGGGCATCTAA

Which reading frame(s) is(are) likely to be the
true reading frame(s)?
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(No Transcript)
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DOT-PLOT Give the coordinates of the boxes to
be filled?
Window size 5 Stringency 5
Window size 5 Stringency 2
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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
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(No Transcript)
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Use the Dotplot to compare chicken ovomucoid
(NM_001112662) to itself
GCACCGGCAGCCGCCTGCAGAGCCGGGCAGTACCTCACCATGGCCATGGC
AGGCGTCTTCGTGCTGTTCT CTTTCGTGCTTTGTGGCTTCCTCCCAGAT
GCTGCCTTTGGGGCTGAGGTGGACTGCAGTAGGTTTCCCAA CGCTACAG
ACAAGGAAGGCAAAGATGTATTGGTTTGCAACAAGGACCTCCGCCCCATC
TGTGGTACCGAT GGAGTCACTTACACCAACGATTGCTTGCTGTGTGCCT
ACAGCATAGAATTTGGAACCAATATCAGCAAAG AGCACGATGGAGAATG
CAAGGAAACTGTTCCTATGAACTGCAGTAGTTATGCCAACACGACAAGCG
AGGA CGGAAAAGTGATGGTCCTCTGCAACAGGGCCTTCAACCCCGTCTG
TGGTACTGATGGAGTCACCTACGAC AATGAGTGTCTGCTGTGTGCCCAC
AAAGTAGAGCAGGGGGCCAGCGTTGACAAGAGGCATGATGGTGGAT GTA
GGAAGGAACTTGCTGCTGTTGACTGCAGCGAGTACCCTAAGCCTGACTGC
ACGGCAGAAGACAGACC TCTCTGTGGCTCCGACAACAAAACATATGGCA
ACAAGTGCAACTTCTGCAATGCAGTCGTGGAAAGCAAC GGGACTCTCAC
TTTAAGCCATTTTGGAAAATGCTGAATATCAGAGCTGAGAGAATTCACCA
CAGGATCCC CACTGGCGAATCCCAGCGAGAGGTCTCACCTCGGTTCATC
TCGCACTCTGGGGAGCTCAGCTCACTCCCG ATTTTCTTTCTCAATAAAC
TAAATCAGCAACAAAAAAAAAA
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What do these parallel lines represent?
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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
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Choose method
default matrix
Set scoring matrix and gap penalties
Paste your sequence
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Open http//www.ch.embnet.org/software/LALIGN_for
m.html

• Use the sequences below and perform a global
  alignment with 5 Opening gap penalty and 0
  Extending gap penalty.
• gtseq1
• GCGACTGTTCCTATGAACTGCAGTAGTTATGCCAACACGACAAGCGAGGA
  CGGAAAAGTGAGTCTGTGGTACTGATGGAGTCACCTACGACGCGAGGACG
  CCAGGTG
• gtseq2
• GCGAGGACGGAAAAGTG

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GLOBAL DOESNT ALWAYS WORK.
GLOBAL
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SOLUTION LOCAL
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Write down the amino acid sequences derived from
all six possible reading frames
of gtseq1 ACTGTCGC gtseqRC GCGACAGT Forward gt_
1 TV gt_2 LS gt_3 CR Reverse gt_1 AT gt_2 RQ
gt_3 DS