Bioinformatics 生物信息学理论和实践 唐继军 jtang@cse.sc 13928761660

1. Bioinformatics生物信息学理论和实践唐继军jtang@cse.sc.edu13928761660Bioinformatics生物信息学理论和实践唐继军jtang@cse.sc.edu13928761660

2. #!/usr/bin/perl $DNA = 'ACGT'; # Next, we print the DNA onto the screen print $DNA, "\n"; print '$DNA\n'; print "$DNA\n"; exit;

3. Do the Math (your 2nd Perl program) #!/usr/bin/perl print "4+5\n"; print 4+5 , "\n"; print "4+5=" , 4+5 , "\n"; [Note: use commas to separate multiple items in a print statement, whitespace is ignored]

4. String Operations • Strings (text) in variables can be used for some math-like operations • Concatenate (join) use the dot . operator $seq1= "ACTG"; $seq2= "GGCTA"; $seq3= $seq1 . $seq2; print $seq3; ACTGGGCTA

5. #!/usr/bin/perl –w $DNA = 'ACGGGAGGACGGGAAAATTACTACGGCATTAGC'; print "Here is the starting DNA:\n\n"; print "$DNA\n\n"; # Transcribe the DNA to RNA by substituting all T's with U's. $RNA = $DNA; $RNA =~ s/T/U/g; # Print the RNA onto the screen print "Here is the result of transcribing the DNA to RNA:\n\n"; print "$RNA\n"; # Exit the program. exit;

6. #!/usr/bin/perl -w $DNA = 'ACGGGAGGACGGGAAAATTACTACGGCATTAGC'; print "$DNA\n\n"; $revcom = reverse $DNA; # See the text for a discussion of tr/// $revcom =~ tr/ACGTacgt/TGCAtgca/; # Print the reverse complement DNA onto the screen print "Here is the reverse complement DNA:\n\n"; print "$revcom\n"; exit;

7. #!/usr/bin/perl -w $proteinfilename = 'NM_021964fragment.pep'; open(PROTEINFILE, $proteinfilename); # First line $protein = <PROTEINFILE>; print “\nHere is the first line of the protein file:\n\n”; print $protein; # Second line $protein = <PROTEINFILE>; print “\nHere is the second line of the protein file:\n\n”; print $protein; # Third line $protein = <PROTEINFILE>; print “\nHere is the third line of the protein file:\n\n”; print $protein; close PROTEINFILE; exit;

8. #!/usr/bin/perl -w # The filename of the file containing the protein sequence data $proteinfilename = 'NM_021964fragment.pep'; # First we have to "open" the file open(PROTEINFILE, $proteinfilename); # Read the protein sequence data from the file, and store it # into the array variable @protein @protein = <PROTEINFILE>; # Print the protein onto the screen print @protein; # Close the file. close PROTEINFILE; exit;

9. #!/usr/bin/perl -w # "scalar context" and "list context" @bases = ('A', 'C', 'G', 'T'); print "@bases\n"; $a = @bases; print $a, "\n"; ($a) = @bases; print $a, "\n"; exit;

10. #!/usr/bin/perl -w # array indexing @bases = ('A', 'C', 'G', 'T'); print "@bases\n"; print $bases[0], "\n"; print $bases[1], "\n"; print $bases[2], "\n"; print $bases[3], "\n"; exit;

11. String functions • Chomp • Length of a string • Substring

12. #!/usr/bin/perl -w $proteinfilename = 'NM_021964fragment.pep'; unless ( open(PROTEINFILE, $proteinfilename) ) { print "Could not open file $proteinfilename!\n"; exit; } while( $protein = <PROTEINFILE> ) { print " #####Here is the next line of the file:\n"; print $protein; } # Close the file. close PROTEINFILE; exit;

13. Comparison • String comparison (are they the same, > or <) • eq (equal ) • ne(not equal ) • ge(greater or equal ) • gt (greater than ) • lt(less than ) • le(less or equal )

14. Conditions • if () {} • elsif() {} • else {}

15. #!/usr/bin/perl –w $word = 'MNIDDKL'; if($word eq 'QSTVSGE') { print "QSTVSGE\n"; } elsif($word eq 'MRQQDMISHDEL') { print "MRQQDMISHDEL\n"; } elsif ( $word eq 'MNIDDKL' ) { print "MNIDDKL-the magic word!\n"; } else { print "Is \”$word\“ a peptide?\n"; } exit;

16. More Conditions

18. $x = 10; $y = -20; if ($x <= 10) { print "1st true\n";} if ($x > 10) {print "2nd true\n";} if ($x <= 10 || $y > -21) {print "3rd true\n";} if ($x > 5 && $y < 0) {print "4th true\n";} if (($x > 5 && $y < 0) || $y > 5) {print "5th true\n";}

19. But • Use ==, <, <=, >, >=, !=, ||, && for numeric numbers • Use eq, lt, le, gt, ge, ne, or, and for string comparisons

21. $x = 10; $y = -20; if ($x le 10) { print "1st true\n";} if ($x gt 5) {print "2nd true\n";} if ($x le 10 || $y gt -21) {print "3rd true\n";} if ($x gt 5 && $y lt 0) {print "4th true\n";} if (($x gt 5 && $y lt 0) || $y gt 5) {print "5th true\n";}

22. #!/usr/bin/perl -w $num = 1234; $str = '1234'; print $num, " ", $str, "\n"; $num_or_str = $num + $str; print $num_or_str, "\n"; $num_or_str = $num . $str; print $num_or_str, "\n"; exit;

23. More Arithmatics • +, -, *, **, /, % • +=, -=, *=, **=, /=, %= • ++, --

24. $x = 10; $x = $x*1.5; print $x*=3, "\n"; print $x++, "\n"; print $x, "\n"; print ++$x, "\n"; print $x, "\n"; print $x % 3, "\n"; print $x**2, "\n";

25. Motif finding • Read a sequence from a fasta file • Ask the user to input a motif • Check if the sequence has the motif

26. #!/usr/bin/perl –w print "Please type the filename: "; $fname = <STDIN>; chomp $fname; open(PROTEINFILE, $fname); $name = <PROTEINFILE>; @protein = <PROTEINFILE>; close PROTEINFILE; $protein = join( '', @protein); $protein =~ s/\s//g; print "Enter a motif to search for: "; $motif = <STDIN>; chomp $motif; if ( $protein =~ /$motif/ ) { print "I found it!\n\n"; } else { print "I couldn\‘t find it.\n\n"; }

27. #!/usr/bin/perl -w print "Please type the filename of the DNA sequence data: "; $dna_filename = <STDIN>; chomp $dna_filename; open(DNAFILE, $dna_filename); $name = <DNAFILE>; @DNA = <DNAFILE>; close DNAFILE; $DNA = join('', @DNA); $DNA =~ s/\s//g; $count_of_CG = 0; $position = 0; while ( $position < length $DNA) { $base = substr($DNA, $position, 1); if ( $base eq 'C' or $base eq 'G') { ++$count_of_CG; } $position++; } print "CG content is ", $count_of_CG/(length $DNA)*100, "%\n";

28. #!/usr/bin/perl –w print "Please type the filename of the DNA sequence data: "; $dna_filename = <STDIN>; chomp $dna_filename; open(DNAFILE, $dna_filename); $name = <DNAFILE>; @DNA = <DNAFILE>; close DNAFILE; $DNA = join('', @DNA); $DNA =~ s/\s//g; $count_of_CG = 0; for ( $position = 0 ; $position < length $DNA ; ++$position ) { $base = substr($DNA, $position, 1); if ( $base eq 'C' or $base eq 'G') { ++$count_of_CG; } } print "CG content is ", $count_of_CG/(length $DNA)*100, "%\n";

29. #!/usr/bin/perl –w print "Please type the filename of the DNA sequence data: "; $dna_filename = <STDIN>; chomp $dna_filename; open(DNAFILE, $dna_filename); $name = <DNAFILE>; @DNA = <DNAFILE>; close DNAFILE; $DNA = join('', @DNA); $DNA =~ s/\s//g; $count_of_CG = 0; while($DNA =~ /c/ig) {$count_of_CG++;} while($DNA =~ /g/ig) {$count_of_CG++;} print "CG content is ", $count_of_CG/(length $DNA)*100, "%\n";

30. #!/usr/bin/perl –w print "Please type the filename of the DNA sequence data: "; $dna_filename = <STDIN>; chomp $dna_filename; open(DNAFILE, $dna_filename); $name = <DNAFILE>; @DNA = <DNAFILE>; close DNAFILE; $DNA = join('', @DNA); $DNA =~ s/\s//g; $count_of_CG = 0; while($DNA =~ /c/i) {$count_of_CG++;} while($DNA =~ /g/ig) {$count_of_CG++;} print "CG content is ", $count_of_CG/(length $DNA)*100, "%\n";

31. Exercise 1 • Ask for a protein file in fasta format • Ask for an amino acid • Count the frequency of that amino acid • TKFHSNAHFYDCWRMLQYQLDMRCMRAISTFSPHCGMEHMPDQTHNQGEMCKPRMWQVSMNQSCNHTPPFRKTYVEWDYMAKALIAPYTLGWLASTCFIW

32. Exercise 2 • Ask for a DNA file in fasta format • Ask for a codon • Count the frequency of that codon • TCGTACTTAGAAATGAGGGTCCGCTTTTGCCCACGCACCTGATCGCTCCTCGTTTGCTTTTAAGAACCGGACGAACCACAGAGCATAAGGAGAACCTCTAGCTGCTTTACAAAGTACTGGTTCCCTTTCCAGCGGGATGCTTTATCTAAACGCAATGAGAGAGGTATTCCTCAGGCCACATCGCTTCCTAGTTCCGCTGGGATCCATCGTTGGCGGCCGAAGCCGCCATTCCATAGTGAGTTCTTCGTCTGTGTCATTCTGTGCCAGATCGTCTGGCAAATAGCCGATCCAGTTTATCTCTCGAAACTATAGTCGTACAGATCGAAATCTTAAGTCAAATCACGCGACTAGACTCAGCTCTATTTTAGTGGTCATGGGTTTTGGTCCCCCCGAGCGGTGCAACCGATTAGGACCATGTAGAACATTAGTTATAAGTCTTCTTTTAAACACAATCTTCCTGCTCAGTGGTACATGGTTATCGTTATTGCTAGCCAGCCTGATAAGTAACACCACCACTGCGACCCTAATGCGCCCTTTCCACGAACACAGGGCTGTCCGATCCTATATTACGACTCCGGGAAGGGGTTCGCAAGTCGCACCCTAAACGATGTTGAAGGCTCAGGATGTACACGCACTAGTACAATACATACGTGTTCCGGCTCTTATCCTGCATCGGAAGCTCAATCATGCATCGCACCAGCGTGTTCGTGTCATCTAGGAGGGGCGCGTAGGATAAATAATTCAATTAAGATATCGTTATGCTAGTATACGCCTACCCGTCACCGGCCAACAGTGTGCAGATGGCGCCACGAGTTACTGGCCCTGATTTCTCCGCTTCTAATACCGCACACTGGGCAATACGAGCTCAAGCCAGTCTCGCAGTAACGCTCATCAGCTAACGAAAGAGTTAGAGGCTCGCTAAATCGCACTGTCGGGGTCCCTTGGGTATTTTACACTAGCGTCAGGTAGGCTAGCATGTGTCTTTCCTTCCAGGGGTATG