using maker_functional_gff with other dbs

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using maker_functional_gff with other dbs

claudia

Hi,

 I am wondering if and how I can go about using a database other than the uniprot-swissprot db for adding blastp hits to a gff3. I have downloaded the nr db from ncbi and created a fasta file however it is very large, I tried to run the maker_functional_gff script with the blast output and the fasta file however it did not work and I get an error stating "uninitialized hash element  $ID at line 142 and 144.


The reason I would like to do this, is by manually blasting proteins against this larger db, I seem to get better hits of which  I would rather use for representation, especially in Gbrowse.

Thanks,
Claudia

( on a related note, the maker_functional_gff script does work with NCBI blast output results as long as the columns are changed or specified)


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Re: using maker_functional_gff with other dbs

Carson Hinton Holt
Re: [maker-devel] using maker_functional_gff with other dbs The script currently only works with UniProt/SwissProt.  In part this is because it is a curated database, so you can have greater confidence in the results.  You would have to modify the script to work with NR.  You might be able to use something like UniProt/TrEMBL which is a larger dataset that includes non-curated genes (like NR).  As long as the FASTA header format is conserved between SwissProt and trEMBL.

I can try and modify the scripts to work with NR, but it will take some time before I can get to it (a week or two).  I just defended my thesis on Monday, and am now taking care of a long list of transition issues.  Let me know and I’ll see what I can do.

Thanks,
Carson




On 5/19/11 1:09 PM, "Dinatale C" <dinatal@...> wrote:

Hi,

 I am wondering if and how I can go about using a database other than the uniprot-swissprot db for adding blastp hits to a gff3. I have downloaded the nr db from ncbi and created a fasta file however it is very large, I tried to run the maker_functional_gff script with the blast output and the fasta file however it did not work and I get an error stating "uninitialized hash element  $ID at line 142 and 144.


The reason I would like to do this, is by manually blasting proteins against this larger db, I seem to get better hits of which  I would rather use for representation, especially in Gbrowse.

Thanks,
Claudia

( on a related note, the maker_functional_gff script does work with NCBI blast output results as long as the columns are changed or specified)


Carson Holt
Graduate Student
Yandell Lab
http:/www.yandell-lab.org/
Eccles Institute of Human Genetics
University of Utah

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