References

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References
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• Assignment Due Friday
• READ
• Ensembl API Tutorial
• http//www.ensembl.org/info/docs/api/core/core_tut
  orial.html

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Cluster Assignment
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References

• Are similar to "pointers" in C
• May be used to build complex data structures
  (such as 2-D arrays)
• Are essentially scalars themselves
• Created with \

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Reference Example

• !/usr/bin/perl
• i 69 scalar
• j \i j is now a scalar "reference" to i
• print j What is this ???
• print "\n"
• print j This "dereferences" a "reference"
• print "\n" meaning, it "accesses" whatever the
  "reference" references (or points to)
• Output
• SCALAR(0x8060224)
• 69

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• !/usr/bin/perl
• i 69 scalar
• j \i j is now a scalar "reference" to i
• print j What is this ???
• print "\n"
• print j This "dereferences" a "reference"
• print "\n" meaning, it "accesses" whatever the
  "reference" references (or points to)
• i 96
• print j Now this prints 96
• print "\n"

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Scalar References

• Scalar reference
• j \i
• Using a scalar reference
• j This is the reference
• j This accesses what the reference is
  pointing to
• Anonymous references
• ref \32
• scooby_ref \"ScoobyDoo"

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References
k
i
Scooby
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m
j
i7 k"Scooby"
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References
k
i
Scooby
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j
m
j \k
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References
k
i
Scooby
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j
m
m j
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References
k
i
Scooby
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j
m
m \j Reference to a reference
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References
k
i
Scooby
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j
m
Value of k through j j Value of k through
m m
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References
k
i
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j
m
k \i Value of i thru m m
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Array References (an array of scalars)

• Creating an array ref
• _at_i (1, 2, 3)
• j \_at_i
• Using an array ref
• k j0 k is first element of array
  1
• The "j" dereferences to an ARRAY, and then the
  "0" accesses the first element of the array

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-gt for Dereferencing

• _at_i (1, 2, 3)
• j \_at_i
• j0 11 change first element of array
  from 1 to 11
• j-gt0 11 ditto (same thing)
• I prefer this notation -- easier to
  read

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Arrays of References (or arrays of arrays)

• j 5
• k 7
• m 8
• _at_i (\j, \k, \m)
• Access the value of j ???
• i0 ???? -- remember this worked when the
  first element of the array was a SCALAR (here the
  first element is a REFERENCE)
• No -- i0 is the reference, NOT i
• i0

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Example

• !/usr/bin/perl
• deepReference2.pl
• j5
• k7
• m8
• _at_i (\j, \k, \m)
• print "First i0 \n"
• print "Second i0 \n"

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Arrays of References (or arrays of arrays)

• Since references are scalars, we can create
  arrays of references
• _at_first (1,2,3,4,5)
• _at_second (10,20,30,40,50)
• _at_third (100,200,300,400,500)
• \_at_ is a "reference"
• _at_numbers (\_at_first,\_at_second,\_at_third) _at_numbers
  is an array of "array references"

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• !/usr/bin/perl
• _at_first (1,2,3,4,5)
• _at_second (10,20,30,40,50)
• _at_third (100,200,300,400,500)
• \_at_ is a "reference"
• _at_numbers (\_at_first,\_at_second,\_at_third)
• foreach i (_at_numbers) i becomes a reference
  to an array
• foreach j (_at_i) _at_ dereferences i (an
  reference to an aray)
• so j is an elemetn of
  an array
• print "j is value in arrayArray\n"
• print "\n"

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Needleman-Wunsch Algorithm

• Dynamic programming solution
• Global, optimal alignment
• Uses a 2D matrix of partially computed alignment
  scores.
• Must select a scoring system for
  matches/mismatches and gaps
• Two phases to the algorithm
• Construction of similarity a matrix
• Recursive traversal of the matrix to construct
  the actual alignment
• An illustration 2 sequences AAAC, AGC

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Algorithm Basics
Match 1 Mismatch -1 Gap -2
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NW Traversal Demonstration
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Example Needleman-Wunsch

• Enter sequence 1
• ATGCCA
• Enter sequence 2
• TGCG
• b matrix
• T G C G
• 0 -1 -2 -3 -4
• A -1 0 0 0 0
• T -2 2 0 0 0
• G -3 0 2 0 2
• C -4 0 0 2 0
• C -5 0 0 2 0
• A -6 0 0 0 0
• d matrix
• T G C G
• 0
• A D D D D
• T D D D D
• G V D H D

• a matrix
• T G C G
• 0 -1 -2 -3 -4
• A -1 0 -1 -2 -3
• T -2 1 0 -1 -2
• G -3 0 3 2 1
• C -4 -1 2 5 4
• C -5 -2 1 4 5
• A -6 -3 0 3 4
• score 4
• Align1 - T G - C G
• Align2 A T G C C A

Use gap -1 mis-match
0 perfect match 2 Make shortest sequence
horizontal Web resources?
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Some code to get started

• sub print_matrix
• my matrixRef shift a ref to an array of
  refs
• my c shift column
• my r shift row
• my i
• my j
• my x
• print "\t\t"
• for(i0iltc-1i)
• print substr(seq1,i,1)."\t"
• print "\n"
• Here's how to access the matrix thru a ref
• matrixRef13 99
• x 0 count thru length of seq2

• !/usr/bin/perl
• use strict
• my _at_a A matrix
• my col 4
• my row 5
• my seq1"TTGGAT"
• my seq2"TTATAGA"
• col length(seq1)1
• row length(seq2)1
• A matrix -- holds calculated scores
• a000

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End