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Rappsilber-Laboratory / xiSPEC_website

http://www.spectrumviewer.org
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show sequence coverage #18

Open colin-combe opened 6 years ago

colin-combe commented 6 years ago

It would be nice to have one panel for each identified protein/s, with the peptide identifications showing the sequence coverage, at least when the protein sequence information is included in the mzIdentML files.

lutzfischer commented 6 years ago

I think you could have coverage to some extend independent of sequence provided (are there cases without this sequence?). Each peptide (assuming it is not a denovo identification) should have the position of the peptide in the protein and the length. So you could fill up the sequence with X and then replace with the identified peptides.

colin-combe commented 6 years ago

I think you could have coverage to some extend independent of sequence provided (are there cases without this sequence?

it was a quote from one of Lars' reviewers

Each peptide (assuming it is not a denovo identification) should have the position

Should but rarely do, because the validator doesn't check for it. (I made an issue at https://github.com/HUPO-PSI/mzIdentML/issues/103)

colin-combe commented 5 years ago

related to https://github.com/Rappsilber-Laboratory/XiSearch/issues/43?

this might not be best place for this issue, though I see I opened it here. (Presumably I had some reason... looks like its from written feedback on xiSPEC.)