Python Bioinformatics : How to count nucleotides in DNA sequences

[@deedarwahab6482]

thanks teacher ir was actually very easy and simple cuz you made it like that even though I don't have any background information about paython.

[@ShadArfMohammed]

Dear Deedar Wahab, Thanks to your comment, Iam happy it was helpful somehow . best regards,

[@Sol-kn6yv]

Dear Dr. Shad Arf How to count mono and di nucleotide from FASTA file and download in csv format in python or other ways? What code will do that.Thank you Sir!

[@ShadArfMohammed]

Dear Sol, I have a video tutorial on that: Below is an example of calculating mono nucleotide percentage from multiple fasta files, kzbin.info/www/bejne/iJ2yq6qXr9uopa8

[@xiaoqingpan1539]

doc, i want to ask a simple question: dna sequences is very long(several lines), when i copy one sequence in pycharm, pycharm can only read one line of the whole sequence. what should i write to let pycharm read the whole sequece?? thank you so much doctor!

[@ShadArfMohammed]

Dear Peter Pan, You can use doc string to input your whole sequence at once. This can be done by flanking your DNA sample sequence with three apostrophes at each end. Best regards.

[@abdalmohaimen3244]

Thanks Mr Arf, It is easy and helpful program.

[@ShadArfMohammed]

Thanks to you too Mr. Abd Almohaimen, glad that you liked it.

[@jansiranim09]

I'm getting the output wrong. While copy paste the nucleotide sequence it is coming discontinuously and after giving double quotes" " at the 1st & last of the sequence only the 1st line of the sequence was changed to green colour rest of the lines remains black colour, beacuse of this my output was not correct. How to change the whole sequence to green colour?

[@ShadArfMohammed]

you can solve the problem using docstring. Three quotation marks flanking your DNA sequence. Watch the video in the link i put in this comment to solve the problem . Link: kzbin.info/www/bejne/q5TKgnyGZbKtqq8

[@priyankavats5362]

its a great tutorial but i am not able to run any of the commands.its asking to define the DNA. can you please explain how to start using python. i am just stuck up with this python.

[@ShadArfMohammed]

Thank you dear Priyanka for your comment, I'm glad you found the material useful. I have another playlist on my channel that starts from the very beginning and how to define variables in python, I suggest you watch that playlist before watching the bioinformatics playlists. Best regards

[@kevinrooney7264]

Hi great tutorial, however when I run my program and input my DNA sequence it appears only the first line of nucleotides are calculated. Is there any way to fix this ? Kind regards

[@ShadArfMohammed]

Hi Kevin, there are some methods to get around that issue. I can suggest 3 methods: 1) you can use docstring method in which you use triple quotation marks around your DNA sequence when assigning your DNA sequence to a variable in the first place, then try to run the calculation algorithm 2) you can save your DNA sequence in a txt file then parse the file using .read() method. I have a specific tutorial on that and you can watch it using the following link below if you would like to give it a try. kzbin.info/www/bejne/Z33EqJ-JgNKVf5I 3) You can use Biopython library's FASTA parsing functionality to do the calculation. Below is another tutorial where I use parsing in it. kzbin.info/www/bejne/aIS5gYWjapxnpdk ----------------------------------------------------------------- Alternatively, if none of the above worked for you kindly paste your code in a comment so that I see what went wrong and try fixing it for you. Kind regards,

[@kevinrooney7264]

@@ShadArfMohammed Hello Shad, thank you for the reply. Apologies for the late response. I seem to have fixed the code and then entire sequence is now read when I run the program. Many thanks Kevin

[@ShadArfMohammed]

Hi Kevin, That's great :) and you're always welcome. Shad.

[@prasanthprasanth8049]

Sir plz upload video for using c programming in bioinformatics

[@ShadArfMohammed]

Dear Prasanth Prasanth, Thanks for your interest in the topic. Python is a C based language on its own. Writing the same codes in C is too difficult and time consuming. Also, there are many libraries for bioinformatics and datascience in Python & R that are hard to find in C. Thus, I specified this channel for Bioinformatics in Python only. However, if by any chance I find learning C easy for biological uses I will definitely upload content on C as well and keep you updated. Best regards,

[@makepistat]

would you mind sharing the video compressed into one video

[@ShadArfMohammed]

Hi, Thanks for your interest in the tutorial, would you like me to combine the playlist? if so, I will do it and send you the link in an email soon. Best regards,

[@makepistat]

@@ShadArfMohammed Yes, i would love that. Thank you

[@giorgibakuradze]

I like it very much. Where can I get more information about this?! I am very interested (also, I am a biologist)

[@ShadArfMohammed]

Dear Giorgi Bakurzade, To get more information about this topic I suggest you read molecular statistics books like DAMBE by Xia or laboratory manuals of bioinformatics. Kind regards,

[@ShadArfMohammed]

Dear Giorgi Bakurzade, To get more information about this topic I suggest you read molecular statistics books like DAMBE by Xia or laboratory manuals of bioinformatics. Kind regards,

[@giorgibakuradze]

@@ShadArfMohammed Thank you very much, I hope that we have a good cooperation.

[@larinbarzan3738]

thank you dear teacher shad..

[@BazyanMRaouf]

Thanks Dr. Shad