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pombase / pombase-chado

PomBase code for accessing Chado
MIT License
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Compare SignalP and Phobius (try to get better coverage of transsit peptides and signal peptides) #1196

Open ValWood opened 3 months ago

ValWood commented 3 months ago

Once https://github.com/pombase/pombase-chado/issues/1195

done, compare signalP ( Phobius (could use the InterPRoAPI for this) DeepSig? and decide thresholds to use to get best coverage.

We still have lots of signal peptides and transit peptides that are not found

Any other tools that could be included?

ValWood commented 3 months ago

Wen I run jackhmmer I get a signal peptide from phobius for https://www.pombase.org/gene/SPBC1E8.03c (I think this is mainly were I am seeing them). We don't have this from phobius in Pombase. So we need to find out what cut off InterPro uses.....

ValWood commented 2 months ago

SignalP:

One of the most widely used tools for signal peptide prediction. SignalP 5.0, the latest version, utilizes deep learning techniques to improve accuracy. It can differentiate between three types of signal peptides: Sec/SPI (bacterial), Sec/SPII (lipoprotein), and Tat/SPI (twin-arginine translocation). Phobius:

Integrates signal peptide prediction with topology prediction. Useful for distinguishing between signal peptides and transmembrane regions. DeepSig:

Uses deep learning methods to predict signal peptides. Claims to offer improved performance over traditional methods like SignalP.

Maybe we should also try DeepSig?