BioInfToolServer

KIPEs

KIPEs (Knowledge-based Identification of Pathway Enzymes) enables the automatic identification and annotation of flavonoid biosynthesis genes/proteins. Users only need to supply a FASTA file with the peptide or transcript sequences. Please read the original publication for details: Pucker et al., 2020. KIPEs is also available for download from a GitHub repository.

Example dataset:

20231217_croton_reduced_example.pep.fasta

MYB_annotator

Our automatic MYB annotation workflow allows users to supply a FASTA file of peptide or transcript sequences to identify the MYB transcription factors. Please have a look at the original publication for details: Pucker, 2022. MYB_annotator is also available for download from a GitHub repository.

Example dataset:

20231217_croton_reduced_example.pep.fasta

CoExp

CoExp enables users to identify co-expressed genes. A list of genes can be provided and the analysis is performed for each of them. All genes with a sufficient co-expression with the candidate gene are returned. A functional annotation file can be provided to assign a functional annotation to the results. CoExp is also available for download from a GitHub repository.

Example dataset:

gene_ids_for_exp_analysis.txt

20230510_reduced_exp_data_set_ath.txt

araport11_annotation_repr_transcript.txt

bHLH_annotator

Our automatic bHLH annotation workflow allows users to supply a FASTA file of peptide or transcript sequences to identify the bHLH transcription factors. Please have a look at the original publication for details: Thoben & Pucker, 2023. bHLH_annotator is also available for download from a GitHub repository.

Example dataset:

20231217_croton_reduced_example.pep.fasta

NAVIP

NAVIP (Neighborhood-Aware Variant Impact Predictor) processes a variant calling format (VCF) file and predicts the functional impact of the sequence variants on annotated genes. Additional details can be found in the original publication: Baasner et al., 2019. NAVIP is also available for download from a GitHub repository.

Example dataset:

20200308_VCC_Nd1_vs_TAIR10.vcf

TAIR10.fa

Araport11_GFF3_genes_transposons.201606.gff

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