Automatically annotating a feature using a genbank file

Question

[Mark]

I’m wondering if there’s a tool out there that I can use for this use case.

I have a linear DNA cassette that I transformed into my organism. This linear cassette is fully sequenced and annotated and has a GenBank file.

The transformed organism will often integrate this cassette with concatamers and partial containers. For example, if I transformed AATTGG into the genome, the integration might be AATTGGAATTGGAAT.

I have a contig assembled that has this integration in it. I’m wondering there’s a tool that can take the FASTA file of the contig, the GENBANK file of the initial cassette, and return a GENBANK file of the contig.

For example. In the initial construct AATTGG has the annotation “promoter” for AAT and “cds” for TGG, I would like the resulting genbank file for AATTGGAATTGGAA to have an annotation something like “promoter.1” “cds.1” “promoter.2” “cds.2” “promoter.3 - partial” or something like that.

[GenoMax]

Not sure if this would be of help. It is certainly not an "automatic" solution: Add gene feature into genebank file

[Pierre Lindenbaum]

Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they all work. If an answer was not really helpful or did not work, provide detailed feedback so others know not to use that answer.

• combine hifiasm and hifiasm-ont assemblies.
• Recommendations for Reference-guided de novo assembly assembly approaches or pipelines?
• Subset reads based on Phred-score ranges
• Best way to assess relatedness of eukaryotic organisms from sequencing reads?
• Convert Long Nanopore reads to Illumina Paired end reads
• Question about Kraken2 core_nt vs nt database results.
• Kmerfinder database with bacteria, archea, and eukaryotic data
• Question about metabolic pathway prediction using only DNA sequencing data
• Strategy to find transgene copy number and integration sites using only Nanopore simplex reads?
• Why use Hi-C and/or Bionano for scaffolding when Nanopore sequencing exists?
• Is there an easy way to scrape a whole bunch of NCBI RefSeq FASTA from NCBI?
• Basic question but how can I search the NCBI Nucleotide database using BLAST CLI
• Recommendations for performing Bulk RNA sequencing on non-model organism with poor genome annotation?
• Does it make sense to use scRNAseq for this experiment?
• Is there a good software to generate test genomics data?
• Best software to get summary statistics from nanopore sequencing runs
• how can i filter a sam file from a paf file
• Does anyone know how to create a sequence annotation figure like this?