An Introduction To Sequence Alignment Algorithms

Cedric Notredame, 2001

Sample Sequences in FASTA format

File 1Protein sequences in FASTA format
File 2Aligned Protein sequences in FASTA format
File 3Two short Proteins sequences in FASTA format
File 4A short Proteins sequences in FASTA format for SW
File 5A short Proteins sequences in FASTA format for SW


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