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compomics / peptide-shaker

Interpretation of proteomics identification results
http://compomics.github.io/projects/peptide-shaker.html
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Feature Request - Protein Sequence Coverage - fasta format #174

Open ulrich-eckhard opened 8 years ago

ulrich-eckhard commented 8 years ago

I guess it is maybe not needed as it can be done by hand, and it is definitely nothing fancy, but think it would be really nice if also PeptideShaker could do it. so something like Mascot does:

image

i know you have the graphical representation, but think a sequence-based one would be just awesome. e.g. with the same color coe that you use right now for the graphical representation. maybe you even have it already and I just missed it. Or do you recommend another tool for it?

image

maybe even just as an additional export option. feasible? all the best from Waterloo this time u

hbarsnes commented 8 years ago

Hi Ulrich,

If you look up PeptideShaker versions from 4-5 years ago you'll find the old school Mascot sequence coverage display. ;)

Pretty sure we still have the code somewhere. This kind of display really only works for shorter protein sequences though, which is partly why we moved to the more flexible and interactive graphical display.

However, I do agree that the sequence based option provides some information that has not been fully transferred to the new display. We've had plans for a long time to look into this, but it has never made it high enough up on our "ordered" list of issues and feature requests. I will keep it in mind though.

Best regards, Harald

ulrich-eckhard commented 8 years ago

totally see the problem with bigger proteins and so on. thus maybe just as a "export" option could be good enough as people wouldn't use it for many proteins at once but rather for selected ones I reckon (e.g. after in-gel digests or so).

re older PeptideShaker and SearchGUI versions: is there a way to download them? i guess not - to keep things simple, just wondering.

On Wed, May 25, 2016 at 4:40 PM, Harald Barsnes notifications@github.com wrote:

Hi Ulrich,

If you look up PeptideShaker versions from 4-5 years ago you'll find the old school Mascot sequence coverage display. ;)

Pretty sure we still have the code somewhere. This kind of display really only works for shorter protein sequences though, which is partly why we moved to the more flexible and interactive graphical display.

However, I do agree that the sequence based option provides some information that has not been fully transferred to the new display. We've had plans for a long time to look into this, but it has never made it high enough up on our "ordered" list of issues and feature requests. I will keep it in mind though.

Best regards, Harald

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/compomics/peptide-shaker/issues/174#issuecomment-221700524

hbarsnes commented 8 years ago

re older PeptideShaker and SearchGUI versions: is there a way to download them?

You can find old versions of PeptideShaker here and old versions of SearchGUI here.

The even older versions were only available as downloads via the Google Code projects and are no longer easily available after Google Code was shut down. But the above links gives you all versions back to July/August 2014, so should be enough? ;)

ulrich-eckhard commented 8 years ago

wow ... nice - thanks. just in case some stuff doesn't work anymore.

as yesterday - wanted to go back to the SG 2.2.2 version I think, because that one did still the mgf to ms2 conversion, but my installation didn't work anymore and didn't have the zipped file anymore.

that's awesome, thanks

On Wed, May 25, 2016 at 4:53 PM, Harald Barsnes notifications@github.com wrote:

re older PeptideShaker and SearchGUI versions: is there a way to download them?

You can find old versions of PeptideShaker here http://genesis.ugent.be/maven2/eu/isas/peptideshaker/PeptideShaker/ and old versions of SearchGUI here http://genesis.ugent.be/maven2/eu/isas/searchgui/SearchGUI/.

The even older versions were only available as downloads via the Google Code projects and are no longer easily available after Google Code was shut down. But the above links gives you all versions back to July/August 2014, so should be enough? ;)

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/compomics/peptide-shaker/issues/174#issuecomment-221704158