PERL for biologists
Here is the list of test programs, that were writting during
the courses so far:
- program 1 The "Hello-World" program in PERL.
Notice that comment lines start with #-sign.
- program 2 shows how to interpret an input
file using regular expressions.
- program 3 opening files for input and
output and substituting regular expressions in string variables.
- program 4 shows the use of if-statements to
direct program flow.
- program 5 while-, until- and for-loops for the
- program 6 array definition and foreach-loops to work on
each element of an array.
- program 7 reading data from a sequence file
and counting the numbers of bases using substr (substring command).
- program 8 the definition of subroutines.
- program 9 how to transfer parameters to subroutines.
- program 10 base composition and dimer compositon.
- program 11 definition of associative arrays.
- program 12 use of associative array to determine
complement of a DNA/RNA sequence.
- program 13 calculate reverse and complement of sequence.
- program 14 use of associative array to
predict protein from DNA sequence.
- program 15 same as before with filtering of
- program 16 demonstrates the production of PNG
graphics by PERL using the GD graphics package.
- program 17 shows how a dotplot of a DNA sequence
can be done.
- program 18 show how a graph of the AT-Content is
calculated and plotted.
- renumber_files.pl renumbers sets of files in a directory.
- align_draw.pl plots alignments in jalview-style.
- translate.cgi Example of a CGI program doing a DNA/RNA translation.