Question: Interproscan did not work for nucleotide
0
gravatar for Sam
3.1 years ago by
Sam0
Sam0 wrote:

I have install latest version of interproscan. It works fine with protein sequences but when I run it with nucleotide sequence (=300 sequences only) it gives issue. My command is ./interproscan.sh -t n -i NuD.fasta And it returns: 04/03/2016 11:06:12:708 Running the following analyses: [jobHAMAP,jobProDom-2006.1,jobPIRSF-3.01,jobPfam,jobSMART-6.2,jobGene3d,jobCoils,jobPrositeProfiles,jobTIGRFAM-15.0,jobPRINTS-42.0,jobSuperFamily-1.75,jobPrositePatterns] Loading file /my_interproscan/interproscan-5.16-55.0/temp/insight-ThinkPad-X230_20160304_110606718_59s7//jobLoadNucleicAcidSequence/orfs.fasta 04/03/2016 11:06:12:897 Running the following analyses: [jobHAMAP,jobProDom-2006.1,jobPIRSF-3.01,jobPfam,jobSMART-6.2,jobGene3d,jobCoils,jobPrositeProfiles,jobTIGRFAM-15.0,jobPRINTS-42.0,jobSuperFamily-1.75,jobPrositePatterns] Available matches will be retrieved from the pre-calculated match lookup service.

Matches for any sequences that are not represented in the lookup service will be calculated locally. 2016-03-04 11:06:13,377 [uk.ac.ebi.interpro.scan.business.sequence.BerkeleyPrecalculatedProteinLookup:283] WARN -

The version of InterProScan you are using is 5.16-55.0 The version of the lookup service you are using is 5.17-56.0 As the data in these versions is not the same, you cannot use this match lookup service. InterProScan will now run locally If you would like to use the match lookup service, you have the following options: i) Download the newest version of InterProScan5 from our FTP site: ftp://ftp.ebi.ac.uk/pub/databases/interpro/ ii) Download the match lookup service for your version of InterProScan from our FTP site and install it locally. You will then need to edit the following property in your configuration file to point to your local installation: precalculated.match.lookup.service.url=

In the meantime, the analysis will continue to run locally.

And it keep on repeating this and nothing happens:

2016-03-04 11:06:15,955 [uk.ac.ebi.interpro.scan.business.sequence.BerkeleyPrecalculatedProteinLookup:283] WARN -

The version of InterProScan you are using is 5.16-55.0 The version of the lookup service you are using is 5.17-56.0 As the data in these versions is not the same, you cannot use this match lookup service. InterProScan will now run locally If you would like to use the match lookup service, you have the following options: i) Download the newest version of InterProScan5 from our FTP site: ftp://ftp.ebi.ac.uk/pub/databases/interpro/ ii) Download the match lookup service for your version of InterProScan from our FTP site and install it locally. You will then need to edit the following property in your configuration file to point to your local installation: precalculated.match.lookup.service.url=

In the meantime, the analysis will continue to run locally.

Can anyone help me. I really don't know what to do even I am not getting any help from any forum. Will be great full for a quick response. Thanks in advance.

interproscan nucleotide • 972 views
ADD COMMENTlink modified 3.1 years ago by Damian Kao15k • written 3.1 years ago by Sam0
0
gravatar for Damian Kao
3.1 years ago by
Damian Kao15k
USA
Damian Kao15k wrote:

The short answer is that you can't input nucleotide sequences directly to Interproscan. Interpro scan uses several HMM databases to scan your sequences. These HMM databases are built based on protein sequence alignments. You can't scan nucleotide sequences with HMMs built from proteins.

What you can do is translate your nucleotide sequences in 6 frames and scan each frame for a potential protein domain.

ADD COMMENTlink written 3.1 years ago by Damian Kao15k
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