SPACE

Detection of Generic Spaced Motifs Using Constrained Submotif Pattern Mining

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Compilation

To compile the source code, issue this command:

$ ./compileall

System Requirements

It runs in UNIX/Linux system, where Perl version 5.8.4 and above should be installed.

Input format, storing input and output files

Input files should be in fasta format, e.g:

Seqname CTGATTTTAAACCC.....(nucleotides should be in one line and no break)

Currently we only accept DNA sequences. Maximum number of sequence allowed = 1000 each of length 5000bp. Before running the program, all the input files should be stored in files/ directory. File extension accepted include: .fasta, .fa, .txt

Supported species. Currently we support 16 species. They are:

Name		Symbol
B.subtilis	bacteria	BBS
G.gallus	chicken	GG
A.thaliana	crest	AT
C.familiaris	dog	CFI
E.coli	ecoli	BEC
D.melanogaster	fruitfly	DM
F.rubripes	fugu	FR
A.nidulans	fungi	AN
H.sapiens	human	HS
A.gambiae	mos_malar	AG
M.musculus	mouse	MM
R.norvegicus	rat	RN
Random Sequence	synthetic	SYNT
C.elegans	worm	CE
S.cerevisiae	yeast	SC
D.rerio	zebrafish	DR

To run the program simple issue the following command:

prompt > perl run_all.pl [filename] [species code]

For example

prompt> perl run_all.pl test.fasta HS

Output will be printed to STDOUT.

Publication

Edward Wijaya, Kanagasabai Rajaraman, Siu Yiu Ming and Sung Wing Kin, Detection of generic spaced motifs using submotif pattern mining, (2007), Bioinformatics, 15;23(12):1476-85. PMID:17483509