1. Introduction to Bioinformatic Computation. Lecture #5 02-15-10
Objectives for today
Regular expressions
Practicing in PERL programming.

2. Compression and decompression
Downloading BLAST
tar (tape archive)
Command line for packing files:
tar -cvf archive.tar dir_names
Command line for unpacking files:
tar –xvf archive.tar
Compression and decompression
gzip and gunzip

3. UNIX commands find / -name your_filename -print
sort –nr -k4 –k7 filename

4. Regular expressions Variable could work inside the regular expression
$c_box = ‘tgatga’;
if ($sequence =~/$c_box/) {
print “C-box inside \n”; }

5. Quiz on Regular Expressions^ $ \s \w \d . + * ?
{3,5}

6. Regular expression modifiers
/pattern/g;
g - find all occurrences
i - turn off case sensitivity
s - do not care about \n inside the string m x e

7. reg_expr1.pl (in LECTURE5)
#!/usr/local/perl
$seq = 'agtctcaggatacaaagtccctacatccggat';
if ($seq =~ /^.{6}([agtc]{4})/ ){print "$1 \n";}

8. reg_expr2.pl (in LECTURE5)
#!/usr/local/perl
#greedy example
$seq = 'agtctcaggatacaaagtccctacatccggat';
if ($seq =~ /^(.+a)/ ) {print "$1 \n";}

9. The match variables for regular expressions (page 121 Learning perl 3rd edition
$& - pattern
$` - string before pattern
$+ - string before pattern and pattern
$’ – string after pattern
Example: preparation of Intron Database from the Exon-Intron Database
prog_introns_exons_IBC2
/home/afedorov/SHEPELEV

10. Example of EID entry (DNA form)
> 2_AAABGLOB protein_id:AAA ; Anadara trapezia beta globin gene, complete cds.; intron(phase:20,size:760,690,intr_sum:1450); exon(size:125,220,114,ex_sum:459); {splice:gtag,gtag}
ATGAGTACTGTGGCCGAGTTGGCGAATGCTGTTGTCAGCAATGCCGATCAAAAAGATTTGCTGAGACTTAGCTGGGGAGT
ATTATCCGTTGATATGGAAGGTACAGGATTGATGCTTATGGCGAAgtaagaacacttaagaatatatgttttagcaattt
ttatttcaattcatgaaatgacattcttatcatgttatttcaagggttaatgcaaaattgcgtgtcaaatgaaatacaat
gacagaaaggatatttgtttcaaacaaatttagccaatgttcccgtgtttcatcagaattatccagttacaagtttttac
ttatgtttaggaagttagttagtatgttttgatttctttcaaaaattattattattctatgagtgattgtacctggtaaa
tctaagtgaaacggtaactatattcaatatttgtttttaaagatgtttcttcaattataaacggctccttttgatatatt
ttcagTTTGTTTAAAACAAGTTCAGCAGCCAGGACAAAATTCGCTCGTCTTGGAGACGTATCAGCTGGTAAAGATAACAG
CAAGCTGAGAGGTCATTCTATCACCTTGATGTACGCCCTCCAGAACTTCATCGATGCTCTCGACAATGTAGACAGATTAA
AGTGTGTTGTAGAAAAATTTGCTGTAAACCACATCAACAGACAAATATCTGCTGACGAATTTGGGgtaagctctttcaaa
gattatgtcttcactttcctcgtgagagcgcacgaagttaatctgatttgtaattttcaagtttttactatgctttggga
tttgaagaagatcgggatagaaaattgacttggtcgggaacacgacttgaatatagataatcacgcagtattttctgttt
taaaaaggccaaatattctagtgaagaaacttaaaaatcgttttcctctgttaggattaggaaccttttatgcatattgt
cttctgttaacatttctgtccattcaactgtaaatgcaagtaaattattttacagtggggagaacaatccctatcaacca
cccaatcaatcaatcaatatttatttacattacagGAAATAGTTGGCCCCTTAAGGCAAACATTAAAGGCTAGGATGGGA
AGTTATTTCGATGAAGATACTGTTTCTGCATGGGCTTCACTTGTTGCTGTTGTCCAGGCTGCATTATAA

11. > EXON_1 1_NT_077402 protein_id:XP_498727
> EXON_1 1_NT_ protein_id:XP_ ; ATGGAGGAGTTCAGAGAAGGTGCAACATTTCTGACCCCCTACAAG
> EXON_2 1_NT_ protein_id:XP_ ; GAAAATGCAGACACAGCACGCCTCTTTGGGACCGCGGTTTATACTTTCGAAGTGCTCGGAGCCCTTCCTCCAGACCGTTCTCCCACACCCCGCTCCAGGGTCTCTCCCGGAGTTACAAGCCTCGCTGTAGGCCCCGGGAACCCAACGCGGTGTCAGAGAAGTGGGGTCCCCTACGAGGGACCAGGAGCTCCGGGCGGGCAGCAGCTGCGGAAGAGCCGCGCGAGGCTTCCCAGAACCCGGCAGGGGCGGGAAGACGCAGGAGTGGGGAGGCGGAACCGGGACCCCGCAGAGCCCGGGTCCCTGCGCCCCACAAGCCTTGGCTTCCCTGCTAGGGCCGGGCAAGGCCGGGTGCAGGGCGCGGCTCCAGGGAGGAAGCTCCGGGGCGAGCCCAAGACGCCTCCCGGGCGGTCGGGGCCCAGCGGCGGCGTTCGCAGTGGAGCCGGGCACCGGGCAGCGGCCGCGGAACACCAGCTTGGCGCAGGCTTCTCGGTCAGGAACG

12. prog_introns_exons_IBC2 Part I: preparing gene sequence
while (<CDS>) {
$c++;
$sign = chop($_);
undef($CDS); undef($EXONS); undef($INTRONS); undef($sequence);
@lines = split("\n", $_);
$id = $lines[0];
if($c == 1) {$id = substr($lines[0],1);}
for $n (1..$#lines) {
chomp ($lines[$n]);
$lines[$n] =~ s/\s//g;
$sequence .= $lines[$n]; }

13. prog_introns_exons_IBC2 Part II: obtaining exons and introns
$count_ex = 0;
while ($sequence) {
$count_ex++;
if ($sequence =~/(^[A-Z]+)/) {
$curr_ex = $+;
$sequence = $';
$CDS .= $curr_ex;
$EXONS .= '> EXON_' . $count_ex . $id . "\n" . $curr_ex . "\n\n"; }
if ($sequence =~/(^[a-z\.]+)/) {
$curr_intr = $+;
$INTRONS .= '> INTRON_' . $count_ex . $id . "\n" . $curr_intr . "\n\n";
unless($curr_ex) {
print 'CHECK YOUR CURRENT SEQUENCE', $id, "\n";
print OUTPUT $sequence, "\n";
die;

14. PRACTICE (homework!)
Write a perl script that detects and report all AGG triplets in the miRNA sequences in the file miRNAmature.fa

15. Regular expressions (chapters 7, 8, 9)
^ beginning of the string
$ end of the string
\s space or tab (\t\n\r\f)
\w word character [a-zA-Z_0-9]
\d any digit [0-9]
. any character
+ one or more characters
* zero or more characters
? zero or one character
{3,5} repeat character from 3 to 5 times