Hi again, and I really appreciate your efforts to help me.
This will be my last post on this for a while - I’m going to spend some time familiarising myself
with AceDB and how to use it. I will also read thoroughly any and all docco (User, Admin
and Dev) I can find on the site - maybe I’m guilty of wanting things to “drop into my lap” too much?
There is one one thing worrying me though, when I kick off
the saceserver - it fires up OK, but issues this warning “sh: 1: uuencode: not found”, and
I would like to know if this could be a problem? Is it related to GNU sharutils? I can
request that that be installed here. I would appreciate knowing if this is normal or
have I disabled some functionality? xace appears to work without “burping”.
OK - I’m starting to grasp this (sort of…). When you say “non-core” - is that species
other than the ones here? ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS240/species/
(New release today - redownload, unzipping… yaaay!). Or is there a defined set of
core species - if so, what is it and/or where is it?
Do I have to load the GFF3s and fasta myself? I don’t mind doing this, if I could
know which data I’m potentially duplicating. Into what do I have to load the non-core
data if I wish to use (for example) the GBrowse, Synteny and other tools to look at it?
My interest is in long range gene and chromosome organisation (intra- and inter-species)
and my fundamental motive for all these pesky questions is how can I be sure that I’m looking
at all of the available data - and finding out what data is available where?
What I would like is to be explicitly told: “Alright Paul, the data for elegans, briggsae, remanei,
japonica and suum (or whatever) is in AceDB and the rest is here (i.e. GFF3 and fasta) and we integrate
the two datasets by doing step1, step2… stepn”.
I’m assuming that the elegans and other core species data is duplicated in their respective species data
in the species download section - as well as in the AceDB downloads.
How does WormBase now interact with non-core species data? Does it? Any links or
whatever to an explanation of this would be appreciated.
<snipped suggestions on how to use AceDB - will look at this myself as mentioned at
p.s. really like the forum software - I’ve used a few of these (notably Oracle forums and orafaq) and
this one is leader of the pack - what is it? I did Google but couldn’t find it.