Help with query_pan_genome

[davidwcleary]

Hello,

Probably a dumb question but is there an easy(?) way to create a multi-fasta alignment using query_pan_genome if you happen to not have a gene name for the sequence you are interested in, example below:

gnl|Prokka|UoS_HiD_208885_contig000017 Prodigal:2.60 CDS 1695 2798 . + 0 ID=UoS_HiD_208885_00745;inference=ab initio prediction:Prodigal:2.60,protein motif:CLUSTERS:PRK10159;locus_tag=UoS_HiD_208885_00745;product=outer membrane phosphoporin protein E;protein_id=gnl|Prokka|UoS_HiD_208885_00745

Thanks for your help,
David

[andrewjpage]

Hi David, You need to find out the name of the cluster. For example if you search the gene presence and absense spreadsheet for UoS_HiD_208885_00745 and take the first cell. It will either be called a gene name or have group_XXX. Regards, Andrew

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On 2 March 2017 at 14:57, davidwcleary ***@***.***> wrote: Hello, Probably a dumb question but is there an easy(?) way to create a multi-fasta alignment using query_pan_genome if you happen to not have a gene name for the sequence you are interested in, example below: gnl|Prokka|UoS_HiD_208885_contig000017 Prodigal:2.60 CDS 1695 2798 . + 0 ID=UoS_HiD_208885_00745;inference=ab initio prediction:Prodigal:2.60,protein motif:CLUSTERS:PRK10159;locus_tag=UoS_HiD_208885_00745;product=outer membrane phosphoporin protein E;protein_id=gnl|Prokka|UoS_HiD_208885_00745 Thanks for your help, David — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#313>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AABeV6aRCnRH9Huv4ZgElPyEe-N4aN57ks5rhtjngaJpZM4MRFyT> .

[davidwcleary]

That's perfect, thanks Andrew.