Hi,
I'm trying to use the prot4EST(James D Wasmuth et al) program in order to find CDS in my EST dataset.
This programme is based on the two programs ESTScan and DECODER(Yoshifumi Fukunishi et al).
Then i need to install ESTScan, my question is "what is the main differents between the 3 version of ESTScan (estscan, ESTSCAN1 and ESTScan2) which are avaible in this project? And which advise me to use with prot4EST?" (version used in the publication is ESTScan_v2.0)
Cheers,
Syl20
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
You probably should use version 2, as that's the one James used when he designed the prot4EST tool.
Version 3 does not bring any new features. It is simply a rewrite in pure C for people who have encountered problems with Perl. Some features are lacking ATM in version 3.
You should not use version 1.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I used ESTScan_v2.0b from the original ftp site. I shall probably port across to version 3 of ESTScan as it's a little cleaner - however this won't happen any time soon...
james
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I used the ESTscan Version 3 with Prot4est.
All is good when we use a existant matrix, but if we want to make matrix in the prot4est pipeline, he fails.
The reason is that in ESTscan version 3, the "buil_model" script is not sufficient alone to make matrix (see the documentation "user guide to develop matrices for ESTscan"). The new procedure to make matrix in this version is to use first the extract_mRNA script then the prepare_data script and finally the build_model script.
One solution is to make the matrix out of the prot4EST pipeline and then enter the matrix location in the prot4EST configuration file. The advantage of this solution is that she allows user to evaluate his matrix before using it.
The other solution is to modify the prot4EST scripts for integrer these two scripts, the modification relates to the estscan_plugin.pl library. In this script there are two modifications to make: the first to add the two new scripts to the pipeline, the second to modify the checking of log files.
- first: line 122 change
system "build_model $conf";
into
system "extract_mRNA $conf";
system "prepare_data $conf";
system "build_model $conf";
- then lines 126->131 change:
my @report=glob('Report/*_process_data.log');
unless ($report[0]) {
print "###error: cannot find the process_data log file!\nPlease email me at nematode.bioinf\@ed.ac.uk\n\n";
die;
}
my $num_coding=&count_codingNt($report[0]);
into
my @report1=glob('Report/*_extract_data.log');
unless ($report1[0]) {
print "###error: cannot find the extract_data log file!\nPlease email me at nematode.bioinf\@ed.ac.uk\n\n";
die;
}
my @report2=glob('Report/*_prepare_data.log');
unless ($report2[0]) {
print "###error: cannot find the prepare_data log file!\nPlease email me at nematode.bioinf\@ed.ac.uk\n\n";
die;
}
my @report3=glob('Report/*_generate_tables.log');
unless ($report3[0]) {
print "###error: cannot find the generate_tables log file!\nPlease email me at nematode.bioinf\@ed.ac.uk\n\n";
die;
}
my $num_coding=&count_codingNt($report2[0]);
other remarks so that prot4EST functions correctly with theESTscan version3 :
- extract_mRNA and prepare_data must be in path
- In this two case, the BT-lib is required and must be installed with EST-scan
- several lines must be changed in the script extract_mRNA (ESTscan 3) so that the RNA downloaded from SRS by the ptrot4est pipeline can be extracted without problems: lines 115, 146, 150 you must change
$e->{_GBtype} ne "mRNA"
into
$e->{_GBtype} !~m/RNA/
cheers,
Sylvain
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi,
I'm trying to use the prot4EST(James D Wasmuth et al) program in order to find CDS in my EST dataset.
This programme is based on the two programs ESTScan and DECODER(Yoshifumi Fukunishi et al).
Then i need to install ESTScan, my question is "what is the main differents between the 3 version of ESTScan (estscan, ESTSCAN1 and ESTScan2) which are avaible in this project? And which advise me to use with prot4EST?" (version used in the publication is ESTScan_v2.0)
Cheers,
Syl20
You probably should use version 2, as that's the one James used when he designed the prot4EST tool.
Version 3 does not bring any new features. It is simply a rewrite in pure C for people who have encountered problems with Perl. Some features are lacking ATM in version 3.
You should not use version 1.
I used ESTScan_v2.0b from the original ftp site. I shall probably port across to version 3 of ESTScan as it's a little cleaner - however this won't happen any time soon...
james
I used the ESTscan Version 3 with Prot4est.
All is good when we use a existant matrix, but if we want to make matrix in the prot4est pipeline, he fails.
The reason is that in ESTscan version 3, the "buil_model" script is not sufficient alone to make matrix (see the documentation "user guide to develop matrices for ESTscan"). The new procedure to make matrix in this version is to use first the extract_mRNA script then the prepare_data script and finally the build_model script.
One solution is to make the matrix out of the prot4EST pipeline and then enter the matrix location in the prot4EST configuration file. The advantage of this solution is that she allows user to evaluate his matrix before using it.
The other solution is to modify the prot4EST scripts for integrer these two scripts, the modification relates to the estscan_plugin.pl library. In this script there are two modifications to make: the first to add the two new scripts to the pipeline, the second to modify the checking of log files.
- first: line 122 change
system "build_model $conf";
into
system "extract_mRNA $conf";
system "prepare_data $conf";
system "build_model $conf";
- then lines 126->131 change:
my @report=glob('Report/*_process_data.log');
unless ($report[0]) {
print "###error: cannot find the process_data log file!\nPlease email me at nematode.bioinf\@ed.ac.uk\n\n";
die;
}
my $num_coding=&count_codingNt($report[0]);
into
my @report1=glob('Report/*_extract_data.log');
unless ($report1[0]) {
print "###error: cannot find the extract_data log file!\nPlease email me at nematode.bioinf\@ed.ac.uk\n\n";
die;
}
my @report2=glob('Report/*_prepare_data.log');
unless ($report2[0]) {
print "###error: cannot find the prepare_data log file!\nPlease email me at nematode.bioinf\@ed.ac.uk\n\n";
die;
}
my @report3=glob('Report/*_generate_tables.log');
unless ($report3[0]) {
print "###error: cannot find the generate_tables log file!\nPlease email me at nematode.bioinf\@ed.ac.uk\n\n";
die;
}
my $num_coding=&count_codingNt($report2[0]);
other remarks so that prot4EST functions correctly with theESTscan version3 :
- extract_mRNA and prepare_data must be in path
- In this two case, the BT-lib is required and must be installed with EST-scan
- several lines must be changed in the script extract_mRNA (ESTscan 3) so that the RNA downloaded from SRS by the ptrot4est pipeline can be extracted without problems: lines 115, 146, 150 you must change
$e->{_GBtype} ne "mRNA"
into
$e->{_GBtype} !~m/RNA/
cheers,
Sylvain