[Bioperl-l] HomoloGene

[Karger, Amir]

> -----Original Message-----
> From: Andrew Macgregor [mailto:andrew@anatomy.otago.ac.nz]
> 
> This is because the eighth column is meant to have a unigene as you 
> say but Dm doesn't have unigene numbers assigned to it so they use 
> the LocusLink ID instead. So it is most definitely possible to find 
> LL in the eighth column.

I'm not satisfied with this answer.

(1) There are a whole lot of records for which they don't include a Unigene
ID. For example, a whole bunch of curated links, like:

Hs|Mm|c|LL.1387 |23598| |LL.12914| | |
http://www.informatics.jax.org/searches/accession_report.cgi?id=MGI:1098280

They still put the LL in the seventh column in this example,and left the
Unigene column blank.

(2 and much more important) Whichever way it's done, why doesn't the README
say so?!
The README's "-The seventh(LL), eighth(UG), and ninth(Accession) fields
correspond
to the second organism." is totally misleading, even if they're putting the
LL in column 8 on purpose.

> 
> Cheers, Andrew.

-Amir
 
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