Replace gene sequence and conserve frame

Hello

How do I use bioinfiormatics toolbox to replace a gene sequence and conserve the reading frame?

G.

[Gavin Seddon]

Hello

my phd is free rad work so pls forgive novice errors.

How do I determine the insertion point and do you know any software for testing the result?

G

Answer 1

[Abhishek Krishna]

Hi,

To replace a gene sequence while conserving the reading frame using a bioinformatics toolbox, you can follow these general steps:

1. Retrieve the gene sequence: Obtain the original gene sequence from a database or a file.

2. Identify the insertion or replacement site: Determine the exact position where you want to insert or replace the sequence. This can be based on the nucleotide position or by searching for specific motifs or features in the gene sequence.

3. Determine the reading frame: The reading frame is crucial for maintaining the correct translation of the gene sequence. It determines the grouping of nucleotides into codons. The reading frame can be identified by locating the start codon (usually ATG) or by aligning the sequence with a known reference sequence.

4. Generate the replacement sequence: Prepare the replacement sequence that you want to insert into the gene. Ensure that the new sequence is in-frame with the existing reading frame. This means that the length of the replacement sequence should be divisible by 3 (to maintain codon alignment).

5. Replace the sequence: Extract the original gene sequence and split it into three reading frames (if necessary). Insert the replacement sequence into the appropriate reading frame, ensuring that it is in-frame with the existing sequence. Concatenate the modified reading frames back together.

6. Validate the modified sequence: Check the modified gene sequence to ensure that it is in the correct reading frame and that the desired replacement has been made accurately. You can use various bioinformatics tools or programming scripts to verify the sequence.

Refer the toolbox documentation - Bioinformatics Toolbox Documentation (mathworks.com) for more information.

I hope this helps!

[Gavin Seddon]

Hello Habhishek, is there a Matlab book that details the finer caviats and perhaps how AI may be incorporated?

G.

[Gavin Seddon]

A book that is useful is

'An Introduction to Machine learning and Bioinformatics'