PBBtools: bioinformatic tools developed by the Plant Biotechnology and Bioinformatics group @ TU Braunschweig

This is a collection of tools and useful scripts developed by the Plant Biotechnology and Bioinformatics research group @ TU Braunschweig. Many of these tools are freely available through our BioinfToolServer. Please get in touch if you have any questions or suggestions for additional features.

KIPEs: Knowledge-based Identification of Pathway Enzymes

Description: This tool facilitates the identification of genes/proteins involved in a particular pathway. KIPEs was initially developed for the annotation of the flavonoid biosynthesis, but can also be applied to other pathways.

Link: KIPEs repository and KIPEs webserver

References: Rempel A & Pucker B (2022). KIPEs3: Automatic annotation of biosynthesis pathways. bioRxiv 2022.06.30.498365; doi:10.1101/2022.06.30.498365.

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, 9, 1103. doi:10.3390/plants9091103.

MYB_annotator: Automatic identification and annotation of MYB transcription factors

Description: This tool facilitates the identification of MYB transcription factors in a given species. Identified MYBs are assigned to well characterized orthologs and a functional annotation is transferred.

Link: MYB_annotator repository and MYB_annotator webserver

Reference: Pucker, B. Automatic identification and annotation of MYB gene family members in plants. BMC Genomics 23, 220 (2022). doi:10.1186/s12864-022-08452-5.

bHLH_annotator: Automatic identification and annotation of bHLH transcription factors

Description: This tool facilitates the identification of bHLH transcription factors in a given species. Identified bHLHs are assigned to well characterized orthologs and a functional annotation is transferred.

Link: bHLH_annotator repository and bHLH_annotator webserver

Reference: Thoben C. and Pucker B. (2023). Automatic annotation of the bHLH gene family in plants. BMC Genomics 24, 780 (2023). doi: 10.1186/s12864-023-09877-2.

CoExp: Co-expression analysis

Description: This tool performs a pairwise co-expression analysis for a given set of genes of interest. All co-expressed genes are identified for this set.

Link: CoExp repository and CoExp webserver

References: Pucker B, Iorizzo M (2023) Apiaceae FNS I originated from F3H through tandem gene duplication. PLOS ONE 18(1): e0280155. doi:10.1371/journal.pone.0280155.

Pucker B., Walker-Hale N., Yim W.C., Cushman J.C., Crumm A., Yang Y., Brockington S. (2022). Evolutionary blocks to anthocyanin accumulation and the loss of an anthocyanin carrier protein in betalain-pigmented Caryophyllales. bioRxiv 2022.10.19.512958; doi:10.1101/2022.10.19.512958.

HeatmapPlotter: Gene expression visualization

Description: This script generates a heatmap for a selection of genes and RNA-seq samples.

Link: HeatmapPlotter repository

References: This repository.

CDS_finder: Identification of Open Reading Frame

Description: This script screens given nucleotide sequences for the longes Open Reading Frame (ORF) / coding sequence (CDS) that could encode a peptide sequence. The longest detected ORF/CDS per input sequence is reported.

Link: CDS_finder repository

Reference: This repository.

TranSeq: Translation of CDS into peptide sequence

Description: This script reads all sequences from a given FASTA file and converts them into the corresponding peptide sequences.

Link: transeq repository

Reference: This repository.

SeqEx: Extracting sequence of interest from FASTA file

Description: This script extracts a specified region on a given sequence from a FASTA file.

Link: seqex repository

Reference: Pucker B, Schilbert H, Schumacher SF. Integrating Molecular Biology and Bioinformatics Education. Journal of Integrative Bioinformatics. 2019;16(3): 20190005. doi:10.1515/jib-2019-0005.

Dotplotter: Visualization of sequence similarity in dot plot

Description: This script compares to sequences and visualizes matches by dots in a 2D plot.

Link: dotplotter repository

Reference: This repository.

MGSE: Mapping-based Genome Size Estimation

Description: This script estimates the size of a plant genome based on the coverage in a read mapping.

Link: MGSE repository

Reference: Pucker B. Mapping-based genome size estimation. bioRxiv 607390; doi:10.1101/607390.

NAVIP: Neighborhood-Aware Variant Impact Predictor

Description: This script predicts the functional impact of sequence variants on the surrounding gene. NAVIP considers all variants in a gene simultaneously to account for their interactions.

Link: NAVIP repository

Reference: Baasner, J.-S., Howard, D., Pucker, B.(2019). Influence of neighboring small sequence variants on functional impact prediction. bioRxiv. doi:10.1101/596718.

Long Read Walker

Description: This script closes the gaps between two contigs in a long read assembly by the extension of overlaps.

Link: LongReadWalker repository

Reference: This repository.

Documentation of methods

Dry lab methods

Wet lab methods