Dear,

We had some troubles to get the next version of the annotation online, due to some bugs in software that would have prevented you to save changes.
But that has been cleared now.

For those that didn't look at the site lately, from now on each can work again on the Tetranychus urticae genome.

The transfer of the genes that were labeled by you got transfered to this new annotation, and in 2/3 of the cases it all went perfectly well.
>From those 2/3, 1/3 was transferred to 100% identical gene models in the new annotation, and an other 1/3 was transfered to a gene model that had at least 1 change in it's coding sequence but was for the rest the same in length.
But be careful: to those that labeled genes only, your genes might be in one of the above categories too.

The last 1/3 are genes (300) that could not be transfered reliably enough, and we therefore would ask each of you to have a look at it (for the genes in your field of interest)
Those differences can be due to several things:
- it was a gene you labeled on the previous annotation without doing anything more, and the model is now maybe correct.
- the sequence changed so that the genes got slightly longer or shorter (different start or stop codon)
- the gene changed to such an extend that the best hit using the old gene was taken, nothing more, and might need more intervention from you.
Those genes that fall under this category are all labeled in the description line with "CHECK MANUALLY".

If one of your genes is labeled as such please have a closer look, and remove the "CHECK MANUALLY" tag from the description line if it is OK for you.

In order to test the system, I did modify/corrected some of those models, but left the "CHECK MANUALLY" tag. Please double check them to make sure the correction I did was indeed the good one.

The expression level that are available via the WIKI are relative to the old (previous annotation). New mapping to the current models is on the way and will be added shortly.

In the attached file you will find a short log-file of the transfer:
- first part
Tetur03g08280<->Tetur07g07950(2009-10-14 09:00:00)
Tetur03g08380<->Tetur07g08020(2009-10-14 09:00:00)
Tetur40g00380<->Tetur37g00410(2009-10-14 09:00:00)
Tetur40g00780<->Tetur37g00740(2009-10-14 09:00:00)
Tetur42g00850<->Tetur05g03090(2009-10-14 09:00:00)
Tetur42g01090<->Tetur05g03390(2009-10-14 09:00:00)
indicates the OLD tetur number and <-> the NEW tetur number
Genes here are not different between the 2 version.

- second part:
CHECK MANUALLY: Tetur06g08250 ->Tetur06g07000(1..109<->1..105:Plus/Plus)
CHECK MANUALLY: Tetur06g09120 ->Tetur06g07750(2794..4133<->1..1340:Plus/Plus)
CHECK MANUALLY: Tetur06g00500 ->Tetur06g00930(110..327<->182..399:Plus/Plus)
Tetur22g03000<->Tetur33g01170(1..2271<->1..2271:Plus/Plus)
CHECK MANUALLY: Tetur28g00910 ->Tetur09g02400(273..2052<->327..2106:Plus/Plus)
Tetur09g06010<->Tetur16g02760(1..264<->1..264:Plus/Plus)
Tetur725g00010<->(..<->..:)
Tetur27g02660<->Tetur25g02140(1..1491<->1..1491:Plus/Plus)
CHECK MANUALLY: Tetur04g02080 ->Tetur04g09430(1..180<->196..375:Plus/Plus)
here one will find which gene should be checked more carefully.

Tetur22g03000<->Tetur33g01170(1..2271<->1..2271:Plus/Plus) Means that both genes should be the same besides some nucleotide changes.
Tetur725g00010<->(..<->..:) Means is missing in the new annotation. Did it disappear??

328 genes are labeled "CHECK MANUALLY"

>From now on you can also ADD new genes with GenomeView. Those genes you add will get a number = last gene on the contig +1 (and will not be intercalated between the others)

As the time for the transfer took more time than anticipated, deadlines are shifted to a later date (Xmas likely) to allow each one of you to do what she/he feels needs to be done.
More about the adapted time line in upcoming mail from Mike.

Best regards
Stephane

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Stephane Rombauts                       Principal Scientific staff

Research group of Bioinformatics & Evolutionary Genomics
Tel:+32 (0)9 331 38 21                        fax:+32 (0)9 3313809
VIB Department of Plant Systems Biology, Ghent University
Technologiepark 927, 9052 Gent, BELGIUM
strom@psb.vib-ugent.be                         http://www.psb.vib-ugent.be
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