Rosalind Consensus and Profile in Bioinformatics with Python [Finding common ancestor]

[@LanaDominkovic]

Thank you for visiting my channel! If you want to support me, the best thing to do is to subscribe and to share out the content :) Make sure to watch my other videos as well. Thank you :)

[@lacapmf]

Awesome, really interesting topic. I am stuck at this Rosalind problem and looking forward seeing the solution and implementation. Tnx

[@LanaDominkovic]

Thanks :)

[@matthevv88]

Very helpful. Keep up good work 🤩

[@LanaDominkovic]

Thanks. I am glad you are enjoying the content

[@kaltenmacher]

Hey, thanks for the tutorial. I had a question. Here we know that n=8 because dataset is small. But for larger dataset, do we need to use len(seq) ? But then how can we implement that for each sequence? Do we need to loop it? Thanks.

[@JasperCove]

Thank you for this super helpful video! Do you have any tips on how to format the output so that Rosalind will accept it? I'm having trouble getting rid of the commas and brackets for the profile matrix's values.

[@LanaDominkovic]

thank you for nice comment, much appriciated:) can you let me know exact problem? as i understood rosalind doesnt accept your answer or?

[@JasperCove]

@@LanaDominkovic Hey! Thank you for replying! I will try to be as clear as possible. If you look at the profile matrix in Rosalind’s sample output, the occurrences of the nucleotides is not separated by commas and is not enclosed in brackets. A: 5 1 0 0 5 5 0 0 C: 0 0 1 4 2 0 6 1 G: 1 1 6 3 0 1 0 0 T: 1 5 0 0 0 1 1 6 Here’s an example of my output which gets rejected by Rosalind: A: [5, 1, 0, 0, 5, 5, 0, 0] C: [0, 0, 1, 4, 2, 0, 6, 1] G: [1, 1, 6, 3, 0, 1, 0, 0] T: [1, 5, 0, 0, 0, 1, 1, 6] Do you see the difference between Rosalind’s sample output and my output? My question is how do I get rid of the brackets and commas in my output so that my profile matrix looks exactly like Rosalind’s sample. If anything is unclear, I will try my best to explain things better. Thank you again for taking the time to understand my question!

[@felsenmeer3004]

for nucleotide in profile_matrix: print(f"{nucleotide}: {' '.join(map(str, profile_matrix[nucleotide]))}") that will look exactly like the sample putput. But it still does'nt by me so @@JasperCove

[@zakiasalod891]

Hi there! Thanks for this. Can you make a video that shows: > Process of a protein sequence FASTA file (as input); and then > Find consensus protein sequence from the above FASTA file Thanks Kind Regards, Zakia Salod

[@LanaDominkovic]

Hey Zakia, thank you for the comment. Maybe while you wait to give you some tips (because I am not sure if I will able to film it so quickly) First you can check how can you read protein sequences from FASTA file. I already did video on that, although that was reading DNA sequences, should be similar for protein sequences. Then for getting consensus protein sequence you can follow this tutorial. Basically what will be different is the dictionary. Now you wont have dict with 4 nucleotides but rather 20 amino acids. Other steps should be the same. Let me know if you tried it and if you get stuck. I can check your code if you link it to me here or on twitter :)

[@zakiasalod891]

Cool. Thanks, sure, will try it out! Much appreciated.

[@Anil-Behera]

Thank you

[@LanaDominkovic]

Thank you for watching :)

[@ishakyusuf4616]

thx

[@LanaDominkovic]

No worries! Thanks for watching :D

[@ishakyusuf4616]

@@LanaDominkovic this helped me so much.

[@Ijazalijin]

👍❤️

[@robertlogan9733]

Come study bioinformatics with me! enc.edu/program/bioinformatics/

[@LanaDominkovic]

Hi Professor Logan. Can you share more details here for anyone interested? I see ENC offers fully online programs. Can you tell me who can apply and are people outside US eligable? I think many people here would be interesting in this bioinformatics program :)

[@user-dx7nk6bl9s]

from Bio import SeqIO #모듈 불러오기 handle = open("chr22.fa","r") #파스타파일 읽기모드로 열기 record = SeqIO.read(handle,"fasta") #read함수이용 파스타읽기 import re #모듈 불러오기 m= re.findall("AWTRTTKRYTY", record.seq) #findall 함수이용 AWTRTTKRYTY 찾고 변수저장 handle.close() #파일 닫기 print(m) #출력 I want to find a consensus sequence using a pasta file, but an error continues to occur in the 6th code. What could be the problem?...