Aggregating peptides - Githubissues

RasmussenLab / pimms

Imputing proteomics data using deep learning models

https://pimms.readthedocs.io/en/latest/

GNU General Public License v3.0

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Aggregating peptides #8

Closed enryH closed 4 months ago

enryH commented 3 years ago

# up to two missed cleavage sites.
peptides = ("ILTERGYSFTTTAEREIVR",
                 "GYSFTTTAEREIVRDIK",
                           "EIVRDIKEK",
                               "DIKEKLCYVALDFEQEMATAASSSSLEK")

[ ] math consecutive sequences (the order is known and leads to consecutive overlaps)
[ ] aggregate peptides in case of overlap with peptides resulting from no miscleavage (having a min lenght of 6), otherwise keep them?
[ ] distinguish observed vs non-observed for aggregation (only consider peptides with evidence)

enryH commented 3 years ago

[ ] check how aggregation of all peptides to gene level work
- Do peptides resulting from "non-missed" cleavage sites overlap between isotopes?
[ ] filter peptides which are non-unique
[ ] filter peptides which are only observed very few times ?
[ ] align peptides along a reference sequence ( Is there one? Are splicing sites just skipped resulting in perfectly alignable isotopes sequences?)