Exploring the Limitations of biobb_dna in Handling Large DNA Sequences

BioBB
1

Hello, Can biobb_dna support a specific length of DNA? I have 90 base pairs, but it only considers 45 base pairs during calculation.

2

Hi Fatemeh,

sorry for the delay in answering your question.

Yes, you should be able to use biobb_dna with structures having >45 base pairs. The trick here is to use the 'sequence' property in the biobb_canal building block. This property is a way to explicitly specify the sequence of the structure analysed. If it is not added, the block tries to automatically extract this information from the previous step (biobb_curves), and this works only with sequences having < 45 base pairs (due to an internal trimming of the information written in the log files by Curves+).

So, could you please try to launch the biobb_canal step using the 'sequence' property like in this example, please:

from biobb_dna.curvesplus.biobb_canal import biobb_canal

canal_out = "canal.out.zip"

seq = "ACGTACGT" # Initialize with the corresponding sequence

prop = {
    'series' : True,
    'histo' : True,
    'sequence' : seq
}

biobb_canal(
    input_cda_file=curves_out_cda,
    input_lis_file=curves_out_lis,
    output_zip_path=canal_out,
    properties=prop
)

Hope it helps!

-Adam-