Lalign

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Lalign DotLet for Pairwise Sequence Alignment
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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
Set scoring matrix and gap penalties
Paste your sequence
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default matrix is PAM250
Paste your sequences
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Exercise A Use Lalign for global and local
alignment
Both human MS2 cell surface antigen (P78325), and
adamalysin II (P34179) from the venom of Crotalus
adamanteus (Eastern diamondback rattlesnake),
contain a zinc protease domain Download the two
protein sequences from NCBI
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Exercise A Use Lalign for global and local
alignment

• Use local alignment with default parameters and
  then
• run global alignment with default parameters.
• What is the different between the two methods?
• b. Which alignment method works better in that
  case?

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Add input sequence
http//www.isrec.isb-sib.ch/java/dotlet/Dotlet.ht
ml
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The conserved domain of MS2 cell surface antigen
(P78325), and adamalysin II (P34179) in the
DotLet program
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Exercise B Use DotLet
Use DotLet to plot the Bacillus subtilis
UTP-glucose-1-phosphate uridylyltransferase gene
against itself.
AAGCTTGTTTAAAAATGGTTTATCCGATATCATAAAAATGTGTAAAAACA
TATTGAAAAGGGTAAATAGAGAATAGTTTA ACCATAAATTTTTTCGATC
ATAAGGAAGGTGCCTTTTAAATGAAAAAAGTACGTAAAGCCATAATTCCA
GCAGCAGGCTT AGGAACACGTTTTCTTCCGGCTACGAAAGCAATGCCGA
AAGAAATGCTTCCTATCGTTGATAAACCTACCATTCAATACA
TAATTGAAGAAGCTGTTGAAGCCGGTATTGAAGATATTATTATCGTAACA
GGAAAAAGCAAGCGTGCGATTGAGGATCAT TTTGATTACTCTCCTGAGC
TTGAAAGAAACCTAGAAGAAAAAGGAAAAACTGAGCTGCTTGAAAAAGTG
AAAAAGGCTTC TAACCTGGCTGACATTCACTATATCCGCCAAAAAGAAC
CTAAAGGTCTCGGACATGCTGTCTGGTGCGCACGCAACTTTA
TCGGCGATGAGCCGTTTGCGGTACTGCTTGGTGACGATATTGTTCAGGCT
GAAACTCCAGGGTTGCGCCAATTAATGGAT GAATATGAAAAAACACTTT
CTTCTATTATCGGTGTTCAGCAGGTGCCCGAAGAAGAAACACACCGCTAC
GGCATTATTGA CCCGCTGACAAGTGAAGGCCGCCGTTATCAGGTGAAAA
ACTTCGTTGAAAAACCGCCTAAAGGCACAGCACCTTCTAATC
TTGCCATCTTAGGCCGTTACGTATTCACGCCTGAGATCTTCATGTATTTA
GAAGAGCAGCAGGTTGGCGCCGGCGGAGAA ATTCAGCTCACAGACGCCA
TTCAAAAGCTGAATGAAATTCAAAGAGTGTTTGCTTACGATTTTGAAGGC
AAGCGTTATGA TGTTGGTGAAAAGCTCGGCTTTATCACAACAACTCTTG
AATTTGCGATGCAGGATAAAGAGCTTCGCGATCAGCTCGTTC
CATTTATGGAAGGTTTACTAAACAAAGAAGAAATCTAAACAAAAAGGCTA
TTGGACATTCATCCAATAGCCTTTTTTTAT TTCAACATCAAAGTCAATG
TATGCTCTTCATTATCAACTGCGAAGACCTGATCAACGGCCTGCCGCAAA
AATTAATAATC CCAGACAAACACACTGATTGTAGAGTTAAACAAACTAA
ATGAAAACATAAATACAAACATGCAGATTAAATAGTAAATAT
CTTGTATTCAATGCAAGCTAAGTAAACACCACTTGCTAAAAGAACAATGA
CTAAACAACCAGCATTACAAAT
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Exercise B Use DotLet
The cursor is positioned at the location of a
translation terminator, which in this case is a
stem-loop in the RNA molecule.
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Dot Plots can also be used to track genome
rearrangements
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Reconstructed