Online Supplementary materials
1) The predicted pre-miRNAs and corresponding miRNAs using triplet-svm (Download)
2) The predicted pre-miRNAs and corresponding miRNAs using RNAmicro (Download)
Application 2. Identification of de novo motifs in conserved regulatory regions (in progress)
News:
PCS-1.5 is released!! A few bugs have been fixed for the shuffling script. (Oct.
5, 2008)
Version 1.0 (Release Nov. 11, 2006)
The perl script to compute PCSs. (Download)
Version 1.1 (Release Dec. 17, 2006)
new PCS program can compute the PCSs of gapped and degenerate k-mers. (Download)
Usage: perl pcs-1.1.pl -b <base_seq.fa> -a <align_seq.net.axt> -o <outputfile>
[-k k] [-s 0|1|2] [-d 0|1|2|3] [-m mode]
New sample files:
The promoter sequences of D. melanogaster
(-1000~+500 at TSSs)
Aligned promoter sequences of D.
melanogaster and D. pseudoobscura (-1000~+500 at TSSs)
Version 1.3 (Release May 17, 2007)
Gapped-PCS program, computing the gapped k-mers and multiple k-mer modes
described in an assigned mode file. (Download)
Usage: perl pcs.pl -b <base_seq.fa> -a <align_seq.net.axt> [-k k] [-s 0|1|2]
-m <modefile>
The format of mode files:
Each line in the mode file describes a specific
gapped mode which should be computed in the program.
The mode may contain one parameter "-1", which
means non-gapped k-mers,
or two parameters "gap position
(0-based position), the number of gaps".
"2,3" means inserted three gaps
(the second parameter) after the third nucleotide (the first parameter):
NNN---NNN
"2,1": NNN-NNN
Example mode file: (Download)
Version 1.4 (Release Jun. 26, 2007)
Revised
Gapped-PCS program, computing the gapped k-mers and multiple k-mer modes
described in an assigned mode file. (Download)
Usage: perl pcs.pl -i <input_align_seq.net.axt> [-k k] [-s 0|1|2] -m <modefile>
The format of mode files:
Each line in the mode file describes a specific
gapped mode which should be computed in the program.
The mode may contain one parameter "-1", which
means non-gapped k-mers,
or two parameters "gap position
(0-based position), the number of gaps".
"2,3" means inserted three gaps
(the second parameter) after the third nucleotide (the first parameter):
NNN---NNN
"2,1": NNN-NNN
Example mode file: (Download)
Example input pairwise alignment: (Download)
A tool (additional tool 2) to evaluate the
significance of conservation by shuffling input sequences has been provided.
Version 1.5 (Release Oct. 5, 2008)
Revised
Gapped-PCS program, computing the gapped k-mers and multiple k-mer modes
described in an assigned mode file. (Download)
Usage: perl pcs-1.5.pl -i <input_align_seq.net.axt> [-k k] [-s 0|1|2]
-c [0|1] -m <modefile>
-c default:0
0: case-insensitive
(the lower-case letters will be included)
1: case-sensitive (the
lower-case letters in the sequence will be masked)
The format of mode files:
Each line in the mode file describes a specific
gapped mode which should be computed in the program.
The mode may contain one parameter "-1", which
means non-gapped k-mers,
or two parameters "gap position
(0-based position), the number of gaps".
"2,3" means inserted three gaps
(the second parameter) after the third nucleotide (the first parameter):
NNN---NNN
"2,1": NNN-NNN
Example mode file: (Download)
Example input pairwise alignment: (Download)
A tool (additional tool 2, version 1.5) to evaluate the
significance of conservation by shuffling input sequences has been provided. Additional Tool 1 (Release May 21, 2007)
The program which can cluster identified conserved motifs according to
sequence similarity. (Download)
Usage: perl pcs_gap_clust.pl <pcs_result_file>
Additional Tool 2 (Release
Jun. 26, 2007, Updated Oct. 5, 2008) The program
which can evaluate the significance of conservation by shuffling input
sequences. (Download)
Latest version 1.5 (pcs-1.5.pl is required) (Download) perl
pcs_shuffle_evaluate-1.5.pl <input_align_file> <mode_file> <strand, 0|1|2>
<length of kmer> <time of shuffling> <case> <outfile> perl
pcs_shuffle_evaluate-1.5.pl dm2droVir1_3utr_070113.fa mode_test 0 7 10 0 pcs.out A third-party Perl script is
needed for the computation. (Download) Washietl S: Alifoldz
algorithm [http://www.tbi.univie.ac.at/papers/SUPPLEMENTS/Alifoldz/] ***Warning: you should cite
the Washietl's work if you use this tool*** Usage: please put the two
Perl scripts at the same directory with the pcs-1.4.pl (lower version is
never allowed). perl
pcs_shuffle_evaluate.pl <input_align_file> <mode_file> <strand, 0|1|2>
<length of kmer> <time of shuffling> <outfile> All
options must be given. perl
pcs_shuffle_evaluate.pl dm2droVir1_3utr_070113.fa mode_test 0 7 10 pcs.out
Usage: perl pcs-1.0.pl -b {base_seq} -a {align_seq} [-k k] [-s 0|1|2]
Sample input files:
3'-UTRs sequences of D. melanogaster
Algined 3'-UTRs sequences of D.
melanogaster and D. pseudoobscura
Notice: {base_seq} file must in single line fasta format!!
-s default:0
0: only scan the positive strand
1: only scan the negative strand
2: scan both strands
-d which degenerate codes will be used, default
0
0: A,C,G,T
1: R(AG),Y(CT),M(AC),K(GT),S(GC),W(AT)
2: B(TGC),D(ATG),H(ATC),V(AGC)
3: N(ACGT)
-m the mode for searching space of motifs, default NNNNNNN
"N" means a nucleotide, defined by the degenerate
codes
"-" means a gap
-k default:6
The length of k-mer used in computation.
-s default:0
0: only scan the positive strand
1: only scan the negative strand
2: scan both strands
-k default:6
The length of k-mer used in computation.
-s default:0
0: only scan the positive strand
1: only scan the negative strand
2: scan both strands
-k default:6
The length of k-mer used in computation.
-s default:0
0: only scan the positive strand
1: only scan the negative strand
2: scan both strands