1. Biology is the science of reverse-engineering life
Living organisms are molecular machines capable of replicating themselves
The functional unit of life is the “cell”
1-100 um in diameter
contains a primary information store: the genome

2. The Structure of a Genome
Generally one or several strands of a polymer, called DNA, packaged into “chromosomes”
Information is encoded as the order of the monomer sub-units (of types “A”, “C”, “G”, “T”) in the linear polymer
Each cell carries the entire genome of the organism.

3. The Nature of DNA Linear, water-soluble, molecular data storage
The polymer is actually “double-stranded”-each strand the “reverse-complement” of the the other
The double strand is 2 nm in diameter
Each monomer unit, “base”, added lengthens the strand by 0.34 nm

4. DNA Storage Density
Genome length of an average bacterium is 2 megabases (Mb)
Human genome 3 gigabases (Gb)
Typical DNA “prep” solution contains about 25 petabytes/ml. (A ml is about 20 drops of a liquid.)

5. Perl and Genomics Good: Bad: Result: frequently middleware
Perl is quick to write
Excellent for parsing
DWIM is good for the typical biologist
Bad:
Not as fast running
Result: frequently middleware

6. My perl scripts 167 in my /bin
Most are for either dealing with system stuff or parsing output from other programs
A few are meant to directly analyze “sequence data”

7. Example Sequence Analysis Program
ssr3.pl
“ssr” is “simple sequence repeat” aka “microsatellite”
E.g:
>Echinomicrosat_01_B04_T7
XXXXXCAGAAGCGCTTCACAATTAAAAGCAAATCATACAAATATGATCAT
CAGGCAGGCTATTTGAACACACTGTTTCGCACTGAACTCATAGTCACATT
TCAGTCGTTCAGTGAGATGATTCATATGGCATAATTTGAACTGACGTTCG
CTCTGACTATCGTTCAGCTCGTTGTGGGCACAATCGTTAGTCAGTTCGTT
CACTCAACCACACACACACACACACACACGGAAACATCAGATTCGAGCTA
AGCTCTTATTACAGCTGATCAGTAGGAGCACTGTTAGACAGTCTACTAAA
TCAATATCAATTATCCCCCCCACACAACCATGGCTTCTGXXXXX

8. Example run of ssr3.pl >Echinomicrosat_01_B04_T7
%ssr3.pl Echinomicrosat_01_B04_T7.fasta
Name Seq Len Range # of repetitions of sub unit Sub unit
Echinomicrosat_01_B04_T of repeat "CA"
>Echinomicrosat_01_B04_T7
XXXXXCAGAAGCGCTTCACAATTAAAAGCAAATCATACAAATATGATCAT
CAGGCAGGCTATTTGAACACACTGTTTCGCACTGAACTCATAGTCACATT
TCAGTCGTTCAGTGAGATGATTCATATGGCATAATTTGAACTGACGTTCG
CTCTGACTATCGTTCAGCTCGTTGTGGGCACAATCGTTAGTCAGTTCGTT
CACTCAACCACACACACACACACACACACGGAAACATCAGATTCGAGCTA
AGCTCTTATTACAGCTGATCAGTAGGAGCACTGTTAGACAGTCTACTAAA
TCAATATCAATTATCCCCCCCACACAACCATGGCTTCTGXXXXX

9. ssr3.pl core routine: while ( $sequences{$x}
=~ m/#Capture each ssr sub-unit within tolerance
#Note "?" for lazy capture. Ensures "AC" is
#the repeat unit instead of "ACAC" for example
([ACGT]{$min_repeat_unit_len,$max_repeat_unit_len}?)
\1{$min_repeat_num,}
/gix
) {
my $repeat_unit = $1;
my $start_of_ssr = $-[0]+1;
my $end_of_ssr = $+[0];
my $ssr = $&;
my $ssr_length = length($ssr)/length($repeat_unit);