[maker-devel] failed to assign putative gene function

[Quanwei Zhang]

Thank you! I used both canonical and isoform of protein sequences from
swiss-prot in the beginning. It reported the error, but later I only used
the canonical protein sequences to build the database and then it worked.

Best
Quanwei

2017-02-20 18:56 GMT-05:00 Carson Holt <carsonhh at gmail.com>:

> You either uses TrEMBL or the UniProtKB Isoform sequence set. Their fasta
> headers are slightly different and will not be parsed correctly,
>
> For example, here is the header as formatted for the same sequence in the
> Swiss-prot dataset download —>
> >sp|Q7Z5M8|AB12B_HUMAN Protein ABHD12B OS=Homo sapiens GN=ABHD12B PE=2 SV=1
>
> I think you used the  UniProtKB Isoform sequence dataset instead.
>
> —Carson
>
>
>
>
>
> > On Feb 13, 2017, at 8:16 AM, Quanwei Zhang <qwzhang0601 at gmail.com>
> wrote:
> >
> > Hello:
> >
> > I am trying to add putative gene function to the predicted gene models.
> Firstly, I use uniProt/Swiss-Prot protein sequences to build the database.
> I used canonical and isoform proteins of human, mouse and rat with the
> script "makeblastdb". Then use "blastp" generated "maker2uni.blastp" whose
> context is as below.
> > maker-CasCan_contig_64815-snap-gene-0.0-mRNA-1
> sp|Q6P5S2|LEG1H_HUMAN    69.97    303    91    0    1    303    1    303
> 7e-164    464
> > snap_masked-CasCan_contig_14203-processed-gene-0.10-mRNA-1
> sp|Q91ZA8|NRARP_MOUSE    99.12    114    1    0    1    114    1    114
> 3e-80    236
> >
> > After that, I am trying to add the protein homology data to the Maker
> gff3 and fasta files with maker_functional_gff and maker_functional_fasta,
> but get the reports as below.
> >
> > Can't parse details from FASTA header: >sp|Q7Z5M8-2|AB12B_HUMAN Isoform
> 2 of Protein ABHD12B OS=Homo sapiens GN=ABHD12B
> >
> > Use of uninitialized value $id in hash element at
> /public/apps/MAKER/2.31.9/bin/maker_functional_gff line 139, <$IN> line
> 39.
> > Use of uninitialized value $id in hash element at
> /public/apps/MAKER/2.31.9/bin/maker_functional_gff line 141, <$IN> line
> 39.
> > Can't parse details from FASTA header: >sp|Q7Z5M8-4|AB12B_HUMAN Isoform
> 4 of Protein ABHD12B OS=Homo sapiens GN=ABHD12B
> >
> > Use of uninitialized value $id in hash element at
> /public/apps/MAKER/2.31.9/bin/maker_functional_gff line 139, <$IN> line
> 45.
> > Use of uninitialized value $id in hash element at
> /public/apps/MAKER/2.31.9/bin/maker_functional_gff line 141, <$IN> line
> 45.
> > Can't parse details from FASTA header: >sp|Q7Z5M8-5|AB12B_HUMAN Isoform
> 5 of Protein ABHD12B OS=Homo sapiens GN=ABHD12B
> > .....
> >
> > I am not sure how to deal with this. I followed the command given in the
> protocol. Any suggestions?
> >
> > Thanks
> >
> > Best
> > Quanwei
> > _______________________________________________
> > maker-devel mailing list
> > maker-devel at box290.bluehost.com
> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20170221/81191253/attachment-0003.html>