PBBtools: bioinformatic tools developed by PuckerLab

This is a collection of tools and useful scripts developed by members of the PuckerLab. 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