Project (BSc/MSc): Automatic annotation of biosynthesis pathways ('KIPEs-X')
Background: We previously developed KIPEs for the automatic identification of the well characterized core genes of the flavonoid biosynthesis in the genome or transcriptome assembly of a new plant species. The flavonoid biosynthesis is involved in many process thus numerous studies need to look at some flavonoid biosynthesis genes. KIPEs performs a phylogenetic analysis which is superior to a frequently used BLAST-only approach regarding the reliability of the results. Additionally, KIPEs checks candidate sequences for the presence of functionally relevant amino acids e.g. the active center.
Objective: The aim of this project is to add extensions to KIPEs to enable the analysis of various additional reactions and other pathways. There are multiple pathways that can be integrated independently which allows multiple students to work on this topic. Here is a list of opportunities, but own ideas are welcome as well:
(1) identification of isoflavonoid biosynthesis genes: this is a branch of the flavonoid biosynthesis that was not included in the initial KIPEs release
(2) identification of the lignin biosynthesis pathway.
Requirements: You should be interested in the respective pathway or in specialized metabolism in general. Some basic knowledge about running scripts on Linux would be helpful.
(1) Pucker, B.; Reiher, F.; Schilbert, H.M. Automatic Identification of Players in the Flavonoid Biosynthesis with Application on the Biomedicinal Plant Croton tiglium. Plants 2020;https://doi.org/10.3390/plants9091103
(2) Rempel, A.; Pucker, B. KIPEs3: Automatic annotation of biosynthesis pathways. bioRxiv 2022.06.30.498365; doi: doi.org/10.1101/2022.06.30.498365
Contact: Boas Pucker