Hello ic23oluk,

Can we have a sample of your data (couple of lines) not the whole file so we can replicate the script and see how we can improve it?

Update: I see from your script $sequence = join ('', @seq); @seq = split ('', $sequence); it looks you are joining and then splitting the array. I am not sure what are you doing there this is why I need to see your input.

Update2: Another possible approach instead of the complex if conditions that you have you could use grep but I need to practice with your code to see what is the expected output as you said that the script works.

Update3: From a quick search online I think you should be looking into getting familiar with BioPerl.

Update4: I think you should be looking for something like this Bio::SeqIO? You can also find some relevant information from similar question Parse DNA fasta file.

Update5: I noticed that you have not provided us yet with a sample of input data and desired output, so I can not really try tackle and help you. But as I was thinking about your problem, I think that you might be interested in using the index function. It will return the sub string position withing your string of data. I case you want to check for multiple sub strings just use the last location and after as a position. Read more about it on the documentation.

Looking forward to your update.

Hope this helps.