Roadmap

1
Roadmap

• The topics
• basic concepts of molecular biology
• Gene, protein
• Central dogma of molecular biology
• PCR, DNA sequencing
• Elements of Perl
• overview of the field
• biological databases and database searching
• sequence alignments
• phylogenetics
• structure prediction
• microarray data analysis

2
Programming and Perlfor BioinformaticsPart I
3
A Taste of Perl print a message

• perltaste.pl Greet the entire world.
• !/usr/bin/perl
• greet the entire world
• x 6e9
• print Hello world!\n
• print All x of you!\n

- command interpretation header
- a comment
- variable assignment statement

- function calls (output statements)
4
Basic Syntax and Data Types

• whitespace doesnt matter to Perl. One can write
  all statements on one line
• All Perl statements end in a semicolon just
  like C
• Comments begin with and Perl ignores
  everything after the until end of line.
• Example this is a comment
• Perl has three basic data types
• scalar
• array (list)
• associative array (hash)

5
Scalars

• Scalar variables begin with followed by an
  identifier
• Example this_is_a_scalar
• An identifier is composed of upper or lower case
  letters, numbers, and underscore '_'. Identifiers
  are case sensitive (like all of Perl)
• progname first_perl
• numOfStudents 4
• sets the content of progname to be the string
  first_perl numOfStudents to be the integer 4

6
Scalar Values

• Numerical Values
• integer 5, 3, 0, -307
• floating point 6.2e9, -4022.33
• hexadecimal/octal 0xd4f, 0477
• binary 0b011011
• NOTE all numerical values stored as
  floating-point numbers (double precision)

7
Do the Math

• Mathematical functions work pretty much as you
  would expect
• 47
• 64
• 43-27
• 256/12
• 2/(3-5)
• Example
• !/usr/bin/perl
• print "45\n"
• print 45 , "\n"
• print "45" , 45 , "\n"
• myNumber 88
• Note use commas to separate multiple items in a
  print statement

45 9 459
What will be the output?
8
Scalar Values

• String values
• Example
• day "Monday "
• print "Happy Monday!\n"
• print "Happy day!\n"
• print 'Happy Monday!\n'
• print 'Happy day!\n'
• Double-quoted interpolates (replaces variable
  name/control character with its value)
• Single-quoted no interpolation done (as-is)

Happy Monday!ltnewlinegt
Happy Monday!ltnewlinegt
Happy Monday!\n
Happy day!\n
What will be the output?
9
String Manipulation

• Concatenation
• dna1 ACTGCGTAGC
• dna2 CTTGCTAT
• juxtapose in a string assignment or print
  statement
• new_dna dna1dna2
• Use the concatenation operator .
• new_dna dna1 . dna2
• Substring
• dna ACTGCGTAGC
• exon1 substr(dna,2,5)

TGCGT
10
Substitution

• DNA transcription T ? U
• Substitution operator s///
• dna GATTACATACACTGTTCA
• rna dna
• rna s/T/U/g GAUUACAUACACUGUUCA
• is a binding operator indicating to exam the
  contents of rna for a match pattern
• Ex Start with dna gaTtACataCACTgttca
• and do the same as above. What will be the output?

11
Example

• transcribe.pl
• dna "gaTtACataCACTgttca"
• rna dna
• rna s/T/U/g
• print "DNA dna\n"
• print "RNA rna\n"
• Does it do what you expect? If not, why not?
• Patterns in substitution are case-sensitive! What
  can we do?
• Convert all letters to upper/lower case
  (preferred when possible)
• If we want to retain mixed case, use
  transliteration/translation operator tr///
• rna tr/tT/uU/ replace all t by u, all T
  by U

12
Case conversion

• string acCGtGcaTGc
• Upper case
• dna uc(string) ACCGTGCATGC
• or dna uc string
• or dna \Ustring
• Lower case
• dna lc(string) accgtgcatgc
• or dna \Lstring
• Sentence case
• dna ucfirst(string) Accgtgcatgc
• or dna \u\Lstring

13
Reverse Complement

• 5- A C G T C T A G C . . . . G C A T -3
• 3- T G C A G A T C G . . . . C G T A -5
• 5- A T G C . . . . G C T A G A C G T -3
• Reverse reverses a string
• string "ACGTCTAGC"
• string reverse(string) "CGATCTGCA
• Complementation use transliteration operator
• string tr/ACGT/TGCA/

14
More on String Manipulation

• String length
• length(dna)
• Index
• index STR,SUBSTR,POSITION
• index(strand, primer, 2)

15
Flow Control

• Conditional Statements
• parts of code executed depending on truth value
  of a logical statement
• truth (logical) values in Perl
• false 0, 0.0, 0e0, , undef, default
• true anything else, default 1
• (a, b) (75, 83)
• if ( a lt b )
• a b
• print Now a b!\n
• if ( a gt b ) print Yes, a gt b!\n
  Compact

16
Comparison Operators
17
Logical Operators
18
if/else/elsif

• allows for multiple branching/outcomes
• randDNA ""
• while ( length(randDNA) lt 200 )
• a rand()
• if ( a lt0.25 )
• randDNA . "A"
• elsif (a lt0.50 )
• randDNA . "C"
• elsif ( a lt 0.75 )
• randDNA . "G"
• else
• randDNA . "T"
• print randDNA

19
Conditional Loops

• while ( statement ) commands
• repeats commands until statement is no longer
  true
• do commands while ( statement )
• same as while, except commands executed as least
  once
• NOTE the after the while statement!!
• Short-circuiting commands next and last
• next jumps to end, do next iteration
• last jumps out of the loop completely

20
while

• Example
• while (alive)
• if (needs_nutrients)
• print Cell needs nutrients\n
• Any problem?

21
for and foreach loops

• Execute a code loop a specified number of times,
  or for a specified list of values
• for and foreach are identical use whichever you
  want
• Incremental loop (C style)
• for ( i0 i lt 50 i )
• x ii
• print "i squared is x.\n"
• Loop over list (foreach loop)
• foreach name ( "Billy", "Bob", "Edwina" )
• print "name is my friend.\n"

22
Basic Data Types

• Perl has three basic data types
• scalar
• array (list)
• associative array (hash)

23
Arrays

• An array (list) is an ordered group of scalar
  values.
• _at_ is used to refer to the entire array
• Example
• (1,2,3) Array of three values 1, 2, and 3
• ("one","two","three") Array of 3 values
  "one", "two", "three"
• _at_names ("mary", "tom", "mark", "john", "jane")
• names 1 ?
• _at_names 1..4

tom
24
Basic Data Types

• Perl has three basic data types
• scalar
• array (list)
• associative array (hash)

25
More on Arrays

• _at_a () empty list
• _at_b (1,2,3) three numbers
• _at_c ("Jan","Joe","Marie") three strings
• _at_d ("Dirk",1.92,46,"20-03-1977") a mixed
  list
• Variables and sublists are interpolated in a list
• _at_b (a,a1,a2) variable interpolation
• _at_c ("Jan",("Joe","Marie")) list
  interpolation
• _at_d ("Dirk",1.92,46,(),"20-03-1977") empty
  list interpolation
• _at_e ( _at_b, _at_c ) same as (1,2,3,"Jan","Joe","M
  arie")
• Practical construction operators (x..y)
• _at_x (1..6) same as (1, 2, 3, 4, 5, 6)
• _at_y (1.2..4.2) same as (1.2, 2.2, 3.2, 4.2,
  5.2)
• _at_z (2..5,8,11..13) same as
  (2,3,4,5,8,11,12,13)

26
Array Manipulations

• reverse Reverses the order of array elements
• _at_a (1, 2, 3)
• _at_b reverse _at_a _at_b (3, 2, 1)
• split Splits a string into a list/array
• line "John Smith 28"
• (first, last, age) split /\s/, line
• DNA "ACGTTTGA"
• _at_DNA split ('', DNA)
• join Joins a list/array into a string
• gene join "", (exon1, exon3)
• name join "-", ("Zhong", "Hui")
• scalar Returns the number of elements in
  _at_array

27
Exercise

• Determine freq of nucleotides
• dna "gaTtACataCACTgttca"
• ?

28
Ex Determine freq of nucleotides

• dna "gaTtACataCACTgttca"
• dna uc(dna) GATTACATACACTGTTCA
• count_A 0
• count_C 0
• count_G 0
• count_T 0
• _at_dna split '', dna
• foreach base (_at_dna)
• if (base eq 'A') count_A
• elsif (base eq 'C') count_C
• elsif (base eq 'G') count_G
• elsif (base eq 'T') count_T
• else print "error!\n"
• print "count of A count_A \n"
• print "count of C count_C \n"
• print "count of G count_G \n"
• print "count of T count_T \n"

29
Filehandles

• File I/O (input/output) reading from/writing to
  files
• Files represented in Perl by a filehandle
  variable
• (for clarity, usu. written as a bare word in
  UPPERCASE)
• Open a file on a filehandle using the open
  function
• for reading (input)
• open INFILE, lt datafile.txt
• or open (INFILE, lt datafile.txt)
• for writing (output), overwriting the file
• open OUTFILE, gt output
• for appending to the end of the file
• open OUTFILE, gtgt output
• Close a file on a filehandle
• Close (OUTFILE)

30
Special Filehandles

• Special files that are always open
• STDIN (standard input)
• input from command window read only
• STDOUT (standard output)
• output to command window write only
• print STDOUT Have fun with Perl!\n
• or just
• print Have fun with Perl!\n

31
Input from Filehandles

• Angle Bracket input operator
• reads one line of input (up to newline/carriage
  return)
• from STDIN
• print "Enter name of protein "
• line ltSTDINgt
• chomp line removes \n from end of line
• print \nYou entered line.\n
• from a file
• open (INPUT, aminos.txt)
• amino1 ltINPUTgt
• amino2 ltINPUTgt
• chomp (amino1, amino2)

32
sequences.fasta

• gtgi145536gbL04574.1Escherichia coli DNA
  polymerase III chi subunit (holC) gene, complete
  cds
• TAACGGCGAAGAGTAATTGCGTCAGGCAAGGCTGTTATTGCCGGATGCGG
  CGTGAACGCCTTATCCGACC
• TACACAGCACTGAACTCGTAGGCCTGATAAGACACAACAGCGTCGCATCA
  GGCGCTGCGGTGTATACCTG
• ATGCGTATTTAAATCCACCACAAGAAGCCCCATTTATGAAAAACGCGACG
  TTCTACCTTCTGGACAATGA
• CACCACCGTCGATGGCTTAAGCGCCGTTGAGCAACTGGTGTGTGAAATTG
  CCGCAGAACGTTGGCGCAGC
• GGTAAGCGCGTGCTCATCGCCTGTGAAGATGAAAAGCAGGCTTACCGGCT
  GGATGAAGCCCTGTGGGCGC
• GTCCGGCAGAAAGCTTTGTTCCGCATAATTTAGCGGGAGAAGGACCGCGC
  GGCGGTGCACCGGTGGAGAT
• CGCCTGGCCGCAAAAGCGTAGCAGCAGCCGGCGCGATATATTGATTAGTC
  TGCGAACAAGCTTTGCAGAT
• TTTGCCACCGCTTTCACAGAAGTGGTAGACTTCGTTCCTTATGAAGATTC
  TCTGAAACAACTGGCGCGCG
• AACGCTATAAAGCCTACCGCGTGGCTGGTTTCAACCTGAATACGGCAACC
  TGGAAATAATGGAAAAGACA
• TATAACCCACAAGATATCGAACAGCCGCTTTACGAGCACTGGGAAAAGCA
  GGGCTACTTTAAGCCTAATG
• GCGATGAAAGCCAGGAAAGTTTCTGCATCATGATCCCGCCGCCGAA

Determine freq of nucleotides
33
Determine frequency of nucleotides

• Input file ltsequences.fastagt
• open (INPUT, "sequences.fasta") open file for
  sequence
• line1 ltINPUTgt
• line2 ltINPUTgt
• line3 ltINPUTgt
• chomp (line2, line3)
• dna line2.line3
• count_A 0
• count_C 0
• count_G 0
• count_T 0
• _at_dna split '', dna
• foreach base (_at_dna)
• if (base eq 'A') count_A
• elsif (base eq 'C') count_C
• elsif (base eq 'G') count_G
• elsif (base eq 'T') count_T