(click here and pg up or down to move inside this frame)
ex2-2.pl circumference with simple <STDIN> input and using Math module
class2.pl
print statement, execute with ` `, scalars
Different control structures (to add numbers from 1 to 50)
ex2-F1, while
2, for
3, foreach
4, infinite loop with while
5, while defined
ex3-1B.pl prime number sieve faster version without modulo
ex3-3.pl program / subrouine to calculate inverse complement of DNA sequence
new.seq input file new1.seq input file
An alternative version using strict and sheltered variables limited to the Subroutine is here
ex3-4.pl determine GC content
(modified from class3.pl)
uses data stored in file,
handles comment lines ala fasta, and
multiple sequence files,
screens for non AGTC characters
new.seq input file new1.seq are possible input files, but you also could use the fasta formated genome of contig sequences
improved .vimrc file is here. Save as .vimrc in your home directory.
class4.pl read file with gi-numbers
make hash (see below)
gi_list.txt input file with GI numbers
class4A.pl Sorts GI hash on keys and values
gi_list.txt input file with GI numbers
simple sort example oligos input with qw//
print with join
ex4-7.pl count oligo frequencies (mod of 3.4) sliding window, hash as counter
new.seq input file
class5.pl runs clustalw alignment of fasta multiple sequence files
glob, system, $!, || or or
input files need to be in the same directory
c100.fa, c101.fa
ex5-2.pl (modification of class4.pl) uses printf gi_list.txt input file with GI numbers
ex5.3.pl copy multiple *.fa files into a single multiple sequence file (uses glob *.fa)
Programs to shatter a multiple sequence file (fasta) into separate files Version A, B, C
A program to calcualte cummulative nucleotide bias along a genome (ex6_3.pl)
A program to calculate (G-C)(G+C) bias in a sliding widow here.
Aprogram to process blastall output (m8/m9 format) (keeps only top hit, calculated other similarity measures) here
LINKS
(right click to open in their own window):
Homology Searching - Lecture slides
A brief collection of UNIX commands
Perl tutorial at http://vergil.chemistry.gatech.edu/
Wikipedia entry on FASTA format
Drop change new line symbols for MACs
Downloads zip from
http://lionel.kr.hs-niederrhein.de/%7Edalitz