How do I make maker combine interproscan and functional_gff results

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How do I make maker combine interproscan and functional_gff results

Emmanuel Nnadi
Hi Carson,
Please I will like to know how to combine the gff results obtained using  ipr_update_gff and the gff obtained using maker_functional_gff?  
For example the ipr_update_gff adds the following to the gff 

scaffold_252    maker   gene    22873   47327   .       -       .       ID=CR513_001491;Name=CR513_001491;Alias=augustus_masked-scaffold_252-processed-gene-0.0;Dbxref=InterPro:IPR000719,Pfam:PF00069;Ontology_term=GO:0004672,GO:0005524,GO:0006468;       ID=CR513scaffold_252    maker   mRNA    22873   47327   .       -       .       ID=CR513_001491-RA;Parent=CR513_001491;Name=CR513_001491-RA;Alias=augustus_masked-scaffold_252-processed-gene-0.0-mRNA-1;Dbxref=InterPro:IPR000719,Pfam:PF00069;Ontology_term=GO:0004672,GO:0005524,GO:0006468;_AED=0.50;_QI=0|0.08|0.04|0.16|1|1|25|0|927;_eAED=0.50;_merge_warning=1; 

While 
maker_functional_gff

scaffold_252    maker   gene    22873   47327   .       -       .       ID=CR513_001491;Name=CR513_001491;Alias=augustus_masked-scaffold_252-processed-gene-0.0;Note=Similar to IREH1: Putative serine/threonine protein kinase IREH1 (Fragment) (Mucuna pruriens OX%3D157652);scaffold_252    maker   mRNA    22873   47327   .       -       .       ID=CR513_001491-RA;Parent=CR513_001491;Name=CR513_001491-RA;Alias=augustus_masked-scaffold_252-processed-gene-0.0-mRNA-1;_AED=0.50;_QI=0|0.08|0.04|0.16|1|1|25|0|927;_eAED=0.50;_merge_warning=1;Note=Similar to IREH1: Putative serine/threonine protein kinase IREH1 (Fragment) (Mucuna pruriens OX%3D157652); (Fragment) (Mucuna pruriens OX%3D157652);


Is there a way of making maker reflect the GO and pfam alongside the functional names?



Also, how can this be reflected in the corresponding protein and transcript fastas?


Thanks for your support.



Nnaemeka Emmanuel Nnadi,Ph.D
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
+2348068124819
Publications: 

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Re: How do I make maker combine interproscan and functional_gff results

Carson Holt-2
The domain info goes in the the database cross reference field according to GFF3 format. We put any functional info in the Note field as it essentially works as a description according the GFF3 best practices. You can also use iprscan2gff3 to create gff3 features corresponding to the position of domains that can be loaded into a browser.  If you want domain or go info inside of the Note field of the GFF3 or in the fasta header, you would need to make your own scripts for that. Note that browsers like Browse can be configured to link out to appropriate websites for values in the Dbxref attribute.

—Carson


On Nov 1, 2020, at 5:45 PM, Emmanuel Nnadi <[hidden email]> wrote:

Hi Carson,
Please I will like to know how to combine the gff results obtained using  ipr_update_gff and the gff obtained using maker_functional_gff?  
For example the ipr_update_gff adds the following to the gff 

scaffold_252    maker   gene    22873   47327   .       -       .       ID=CR513_001491;Name=CR513_001491;Alias=augustus_masked-scaffold_252-processed-gene-0.0;Dbxref=InterPro:IPR000719,Pfam:PF00069;Ontology_term=GO:0004672,GO:0005524,GO:0006468;       ID=CR513scaffold_252    maker   mRNA    22873   47327   .       -       .       ID=CR513_001491-RA;Parent=CR513_001491;Name=CR513_001491-RA;Alias=augustus_masked-scaffold_252-processed-gene-0.0-mRNA-1;Dbxref=InterPro:IPR000719,Pfam:PF00069;Ontology_term=GO:0004672,GO:0005524,GO:0006468;_AED=0.50;_QI=0|0.08|0.04|0.16|1|1|25|0|927;_eAED=0.50;_merge_warning=1; 

While 
maker_functional_gff
scaffold_252    maker   gene    22873   47327   .       -       .       ID=CR513_001491;Name=CR513_001491;Alias=augustus_masked-scaffold_252-processed-gene-0.0;Note=Similar to IREH1: Putative serine/threonine protein kinase IREH1 (Fragment) (Mucuna pruriens OX%3D157652);scaffold_252    maker   mRNA    22873   47327   .       -       .       ID=CR513_001491-RA;Parent=CR513_001491;Name=CR513_001491-RA;Alias=augustus_masked-scaffold_252-processed-gene-0.0-mRNA-1;_AED=0.50;_QI=0|0.08|0.04|0.16|1|1|25|0|927;_eAED=0.50;_merge_warning=1;Note=Similar to IREH1: Putative serine/threonine protein kinase IREH1 (Fragment) (Mucuna pruriens OX%3D157652); (Fragment) (Mucuna pruriens OX%3D157652);

Is there a way of making maker reflect the GO and pfam alongside the functional names?


Also, how can this be reflected in the corresponding protein and transcript fastas?

Thanks for your support.


Nnaemeka Emmanuel Nnadi,Ph.D
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
+2348068124819
Publications: 


_______________________________________________
maker-devel mailing list
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

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