Bioinformatics Algorithms In Perl, Front end, Cedric Notredame 2001

Perl Implementation of some basic sequence
comparison algorithms.

PLEASE NOTE: These algorithms are only meant to be
used as pedagogic support. They are simplified versions of the real stuff
and are not meant to be used for research purposes.

Program

Description

Usage

hello_World.pl Hello World… hello_world bubble_sort.pl sorts number in increasing order bubble_sort dna2rna.pl translate DNA sequences into RNA sequences bubble_sort file
file : Sequence(s) in FASTA format.
output: Sequence(s) in FASTA format. dotter.pl makes an ascii dotter of two sequences dotter.pl file(s)
file(s): Sequence(s) in FASTA format.
output: dot-matrix. score_aln.pl scores a pair-wise aln score_aln.pl file(s)
file(s): Aligned Sequence(s) in FASTA format. nw.pl Global aln of two sequences nw.pl file1 file2
files: Aligned Sequence(s) in FASTA format.One sequence
per file
output:Aligned sequences in FASTA sw.pl Local aln of two sequences sw.pl file1 file2
files: Aligned Sequence(s) in FASTA format.One sequence
per file kdotter.pl Computation of the common Ktup (k=1) between two
sequences kdotter.pl file
files: Sequence(s) in FASTA score_maln.pl Star and Sp evaluation of a maln score_maln.pl file
files: Aln Sequence(s) in FASTA pnw.pl Global Alignment of two profiles kpnw.pl file1 file2
files: Aln Sequence(s) in FASTA kpnw.pl Global Alignment of two profiles in time linear with
the number of sequences kpnw.pl file1 file2
files: Aln Sequence(s) in FASTA score_maln.pl Star and Sp evaluation of a maln score_maln.pl file1
files: Aln Sequence(s) in FASTA maln.pl Align N sequences in the provided order. Uses pnw.pl maln.pl file1
files:Sequence(s) in FASTA

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