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Introduce heterologous genes into database

asked 2020-05-03 11:29:47 -0500

anonymous user


I have a number of heterologous genes I would like to include in a private genome database, so that can include in pathway annotations (for pathway engineering). As there is not necessarily a specific chromosomal location to place them (could be arbitrary I suppose at beginning or end of genome) what would be a recommendation on how to handle this. Right now I can enter a new gene or protein but the associated sequence I figure can only go in the comment.

Maybe this is already straightforward but I can't seem to find a way without crashing program looking for a location to insert gene.

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answered 2020-05-03 13:22:42 -0500

Suzanne Paley gravatar image

Hi, we don't really support this kind of thing, so any solution will be rather ad hoc. The easiest thing to do would be, as you suggested, creating the new genes or proteins without a chromosomal location. As you discovered, this would leave them them without a proper sequence, except for whatever you put in the comment field. Another alternative would be to create one or more artificial chromosomes or contigs (you could either combine all your heterologous genes into a single artificial chromosome, or generate a different contig for each one, or anything in between). That would let you provide one or more sequence files that contained all the sequences you want to include. The map positions would of course be bogus. This (a single artificial chromosome) is actually the solution we employ for our pan-genome databases, for all genes that don't have orthologs in the primary strain. It is admittedly imperfect, and takes some work to assemble and incorporate, but I don't think we have a better solution at this time.

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Asked: 2020-05-03 11:29:47 -0500

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Last updated: May 03