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Make sure all the data files are accessible in the server. #6

Open timlevine opened 6 years ago

timlevine commented 6 years ago

Urn1 = YPR152C : does the server show the 2nd WW domain in residues 50-90?

ilectra commented 6 years ago

Do you mean this? @timlevine ypr152c

timlevine commented 6 years ago

yes - and it's "perfect" having the hits between residues 55 and 90 (which is missing elsewhere) Tim

ilectra commented 6 years ago

@timlevine The list of proteins we don't have results for:

YPLCTy4-1.0.ssw11.hhr YDR406W.0.ssw11.hhr YGR199W.0.ssw11.hhr Q0050.0.ssw11.hhr YGR003W.0.ssw11.hhr YAR062W.0.ssw11.hhr YCL011C.0.ssw11.hhr YNR047W.0.ssw11.hhr YKL203C.0.ssw11.hhr YJL207C.0.ssw11.hhr YOR116C.0.ssw11.hhr YBL099W.0.ssw11.hhr YDR145W.0.ssw11.hhr YOR393W.0.ssw11.hhr YBL088C.0.ssw11.hhr YDR422C.0.ssw11.hhr YDR484W.0.ssw11.hhr YMR284W.0.ssw11.hhr YNL163C.0.ssw11.hhr YBR276C.0.ssw11.hhr YGR204W.0.ssw11.hhr YPL249C.0.ssw11.hhr YDR416W.0.ssw11.hhr YKL164C.0.ssw11.hhr YOR343W-B.0.ssw11.hhr YLR096W.0.ssw11.hhr YOR251C.0.ssw11.hhr YIL092W.0.ssw11.hhr YOR162C.0.ssw11.hhr YMR013C.0.ssw11.hhr YGL097W.0.ssw11.hhr YAL026C.0.ssw11.hhr YLL001W.0.ssw11.hhr YIL147C.0.ssw11.hhr YAL008W.0.ssw11.hhr YGL062W.0.ssw11.hhr YGR240C.0.ssw11.hhr YKL209C.0.ssw11.hhr YKL188C.0.ssw11.hhr YPL226W.0.ssw11.hhr YGR281W.0.ssw11.hhr YBR084W.0.ssw11.hhr YLR398C.0.ssw11.hhr YLR163C.0.ssw11.hhr YPL137C.0.ssw11.hhr YER132C.0.ssw11.hhr YMR176W.0.ssw11.hhr YGR061C.0.ssw11.hhr YGL100W.0.ssw11.hhr YMR296C.0.ssw11.hhr YER164W.0.ssw11.hhr YOL152W.0.ssw11.hhr YPR009W.0.ssw11.hhr YGR245C.0.ssw11.hhr YFL007W.0.ssw11.hhr YDR359C.0.ssw11.hhr YEL060C.0.ssw11.hhr YBR225W.0.ssw11.hhr YDL040C.0.ssw11.hhr YJR066W.0.ssw11.hhr YFL057C.0.ssw11.hhr YOL021C.0.ssw11.hhr YPR032W.0.ssw11.hhr YGL197W.0.ssw11.hhr YNR033W.0.ssw11.hhr YGL086W.0.ssw11.hhr YAR019C.0.ssw11.hhr YOL123W.0.ssw11.hhr

timlevine commented 6 years ago

Hi Ilektra

I repeated the search online with Pdr15 (Yrd406w) and it worked (see https://toolkit.tuebingen.mpg.de/#/jobs/pdr15).

There are 67 yeast genes in the list - I can't make out the top entry (YPLCTy4-1)

Their average number of annotated domains in SGD is 9.1 compared to 4.4 for the 6717 in a list I found (this must contain the dubious ORFs - if you have an updated list excluding those, please send!). This increase in domain number is statistically significant (p=1e-10), so on the whole these proteins are more complicated than average.

There is little difference between the file of hits generated for one I tried and what a "sister" protein (Pdr10) generated, so it seems unlikely that there is something about the data flow/file size being a bit too big.

Rather than go through the other 66, we should decide if you can run them again (only 1%) or if you want me to run them online and send you the files!!!!!

All the best, Tim

From: Ilektra Christidi notifications@github.com Sent: Monday, February 5, 2018 2:59 PM To: UCL/HHyeast-server Cc: Levine, Tim; Mention Subject: Re: [UCL/HHyeast-server] Make sure all the data files are accessible in the server. (#6)

@timlevinehttps://github.com/timlevine The list of proteins we don't have results for:

YPLCTy4-1.0.ssw11.hhr YDR406W.0.ssw11.hhr YGR199W.0.ssw11.hhr Q0050.0.ssw11.hhr YGR003W.0.ssw11.hhr YAR062W.0.ssw11.hhr YCL011C.0.ssw11.hhr YNR047W.0.ssw11.hhr YKL203C.0.ssw11.hhr YJL207C.0.ssw11.hhr YOR116C.0.ssw11.hhr YBL099W.0.ssw11.hhr YDR145W.0.ssw11.hhr YOR393W.0.ssw11.hhr YBL088C.0.ssw11.hhr YDR422C.0.ssw11.hhr YDR484W.0.ssw11.hhr YMR284W.0.ssw11.hhr YNL163C.0.ssw11.hhr YBR276C.0.ssw11.hhr YGR204W.0.ssw11.hhr YPL249C.0.ssw11.hhr YDR416W.0.ssw11.hhr YKL164C.0.ssw11.hhr YOR343W-B.0.ssw11.hhr YLR096W.0.ssw11.hhr YOR251C.0.ssw11.hhr YIL092W.0.ssw11.hhr YOR162C.0.ssw11.hhr YMR013C.0.ssw11.hhr YGL097W.0.ssw11.hhr YAL026C.0.ssw11.hhr YLL001W.0.ssw11.hhr YIL147C.0.ssw11.hhr YAL008W.0.ssw11.hhr YGL062W.0.ssw11.hhr YGR240C.0.ssw11.hhr YKL209C.0.ssw11.hhr YKL188C.0.ssw11.hhr YPL226W.0.ssw11.hhr YGR281W.0.ssw11.hhr YBR084W.0.ssw11.hhr YLR398C.0.ssw11.hhr YLR163C.0.ssw11.hhr YPL137C.0.ssw11.hhr YER132C.0.ssw11.hhr YMR176W.0.ssw11.hhr YGR061C.0.ssw11.hhr YGL100W.0.ssw11.hhr YMR296C.0.ssw11.hhr YER164W.0.ssw11.hhr YOL152W.0.ssw11.hhr YPR009W.0.ssw11.hhr YGR245C.0.ssw11.hhr YFL007W.0.ssw11.hhr YDR359C.0.ssw11.hhr YEL060C.0.ssw11.hhr YBR225W.0.ssw11.hhr YDL040C.0.ssw11.hhr YJR066W.0.ssw11.hhr YFL057C.0.ssw11.hhr YOL021C.0.ssw11.hhr YPR032W.0.ssw11.hhr YGL197W.0.ssw11.hhr YNR033W.0.ssw11.hhr YGL086W.0.ssw11.hhr YAR019C.0.ssw11.hhr YOL123W.0.ssw11.hhr

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ilectra commented 5 years ago

The re-processed data that was missing is ready, I need to upload them a.s.a.p.!

ORF's reported missing by Tim: YAL008W, YGL197W (in above list) YOR376W (missing altogether, need to investigate)

timlevine commented 5 years ago

Thanks for that.

Will HHyeast have a simple URL by December 17?