Matches in SemOpenAlex for { <https://semopenalex.org/work/W3170354148> ?p ?o ?g. }
Showing items 1 to 81 of
81
with 100 items per page.
- W3170354148 abstract "Abstract Summary We have implemented the pypgatk package and the pgdb workflow to create proteogenomics databases based on ENSEMBL resources. The tools allow the generation of protein sequences from novel protein-coding transcripts by performing a three-frame translation of pseudogenes, lncRNAs, and other non-canonical transcripts, such as those produced by alternative splicing events. It also includes exonic out-of-frame translation from otherwise canonical protein-coding mRNAs. Moreover, the tool enables the generation of variant protein sequences from multiple sources of genomic variants including COSMIC, cBioportal, gnomAD, and mutations detected from sequencing of patient samples. pypgatk and pgdb provide multiple functionalities for database handling, notably optimized target/decoy generation by the algorithm DecoyPyrat . Finally, we perform a reanalysis of four public datasets in PRIDE by generating cell-type specific databases for 65 cell lines using the pypgatk and pgdb workflow, revealing a wealth of non-canonical or cryptic peptides amounting to more than 10% of the total number of peptides identified (43,501 out of 402,512). Availability The software is freely available. pypgatk : ( https://github.com/bigbio/py-pgatk/ ), and pgdb : ( https://github.com/nf-core/pgdb ) Contact Yasset Perez-Riverol ( yperez@ebi.ac.uk ), Rui Branca ( rui.mamede-branca@ki.se ) Supplementary information Supplementary data are available online." @default.
- W3170354148 created "2021-06-22" @default.
- W3170354148 creator A5036264996 @default.
- W3170354148 creator A5038875783 @default.
- W3170354148 creator A5050114104 @default.
- W3170354148 creator A5051446198 @default.
- W3170354148 creator A5053274567 @default.
- W3170354148 creator A5055658645 @default.
- W3170354148 creator A5058153415 @default.
- W3170354148 date "2021-06-09" @default.
- W3170354148 modified "2023-10-16" @default.
- W3170354148 title "Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides" @default.
- W3170354148 cites W2040415319 @default.
- W3170354148 cites W2079563665 @default.
- W3170354148 cites W2807248405 @default.
- W3170354148 cites W2899760200 @default.
- W3170354148 cites W2994150660 @default.
- W3170354148 cites W3134022400 @default.
- W3170354148 doi "https://doi.org/10.1101/2021.06.08.447496" @default.
- W3170354148 hasPublicationYear "2021" @default.
- W3170354148 type Work @default.
- W3170354148 sameAs 3170354148 @default.
- W3170354148 citedByCount "2" @default.
- W3170354148 countsByYear W31703541482022 @default.
- W3170354148 countsByYear W31703541482023 @default.
- W3170354148 crossrefType "posted-content" @default.
- W3170354148 hasAuthorship W3170354148A5036264996 @default.
- W3170354148 hasAuthorship W3170354148A5038875783 @default.
- W3170354148 hasAuthorship W3170354148A5050114104 @default.
- W3170354148 hasAuthorship W3170354148A5051446198 @default.
- W3170354148 hasAuthorship W3170354148A5053274567 @default.
- W3170354148 hasAuthorship W3170354148A5055658645 @default.
- W3170354148 hasAuthorship W3170354148A5058153415 @default.
- W3170354148 hasBestOaLocation W31703541481 @default.
- W3170354148 hasConcept C104317684 @default.
- W3170354148 hasConcept C141231307 @default.
- W3170354148 hasConcept C141674004 @default.
- W3170354148 hasConcept C145741570 @default.
- W3170354148 hasConcept C177212765 @default.
- W3170354148 hasConcept C189206191 @default.
- W3170354148 hasConcept C202264299 @default.
- W3170354148 hasConcept C41008148 @default.
- W3170354148 hasConcept C54355233 @default.
- W3170354148 hasConcept C54458228 @default.
- W3170354148 hasConcept C67705224 @default.
- W3170354148 hasConcept C70721500 @default.
- W3170354148 hasConcept C77088390 @default.
- W3170354148 hasConcept C86803240 @default.
- W3170354148 hasConceptScore W3170354148C104317684 @default.
- W3170354148 hasConceptScore W3170354148C141231307 @default.
- W3170354148 hasConceptScore W3170354148C141674004 @default.
- W3170354148 hasConceptScore W3170354148C145741570 @default.
- W3170354148 hasConceptScore W3170354148C177212765 @default.
- W3170354148 hasConceptScore W3170354148C189206191 @default.
- W3170354148 hasConceptScore W3170354148C202264299 @default.
- W3170354148 hasConceptScore W3170354148C41008148 @default.
- W3170354148 hasConceptScore W3170354148C54355233 @default.
- W3170354148 hasConceptScore W3170354148C54458228 @default.
- W3170354148 hasConceptScore W3170354148C67705224 @default.
- W3170354148 hasConceptScore W3170354148C70721500 @default.
- W3170354148 hasConceptScore W3170354148C77088390 @default.
- W3170354148 hasConceptScore W3170354148C86803240 @default.
- W3170354148 hasLocation W31703541481 @default.
- W3170354148 hasLocation W31703541482 @default.
- W3170354148 hasLocation W31703541483 @default.
- W3170354148 hasOpenAccess W3170354148 @default.
- W3170354148 hasPrimaryLocation W31703541481 @default.
- W3170354148 hasRelatedWork W1653665192 @default.
- W3170354148 hasRelatedWork W2122064342 @default.
- W3170354148 hasRelatedWork W2156467546 @default.
- W3170354148 hasRelatedWork W2803476996 @default.
- W3170354148 hasRelatedWork W2910409918 @default.
- W3170354148 hasRelatedWork W2947085902 @default.
- W3170354148 hasRelatedWork W3119905834 @default.
- W3170354148 hasRelatedWork W4205146010 @default.
- W3170354148 hasRelatedWork W4226024912 @default.
- W3170354148 hasRelatedWork W4288064090 @default.
- W3170354148 isParatext "false" @default.
- W3170354148 isRetracted "false" @default.
- W3170354148 magId "3170354148" @default.
- W3170354148 workType "article" @default.