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@samboesen6446 3 күн бұрын
this is awesome. All of the solutions online seem incredibly bulky and involve and unnecessary amount of steps. I love how simple you made this. How might a junior in college break into the field of bioinformatics? Are projects and skills more important the strong networking?
@vitorlima1092 2 ай бұрын
Hello and thank you from Brazil!
@kaltenmacher 3 ай бұрын
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.
@mateuslemos126 3 ай бұрын
This video is awesome. Crazy to think it was uploaded 2 years ago. I can't wait to check your most recent videos!
@mateuslemos126 3 ай бұрын
This is a very insightful video! Thank you. Some programs do the same thing too. FastQC gives off all the quality stats you've mentioned in a drop of a hat.
@jeanjacqueskubwimana8362 4 ай бұрын
Hey Lana Lomodovic, How can i contact you in case i have a question to ask?
@GauravSharma-gd7pd 4 ай бұрын
Hello ma'am. I am getting this error. Can you help me out? Traceback (most recent call last): File "<stdin>", line 1, in <module> File "C:\Users\USER\AppData\Local\Programs\Python\Python311\Lib\site-packages\Bio\SeqIO\__init__.py", line 625, in parse return iterator_generator(handle) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\USER\AppData\Local\Programs\Python\Python311\Lib\site-packages\Bio\SeqIO\FastaIO.py", line 187, in __init__ super().__init__(source, mode="t", fmt="Fasta") File "C:\Users\USER\AppData\Local\Programs\Python\Python311\Lib\site-packages\Bio\SeqIO\Interfaces.py", line 64, in __init__ self.stream = open(source, "r" + mode) ^^^^^^^^^^^^^^^^^^^^^^^^ FileNotFoundError: [Errno 2] No such file or directory: 'sequence.fasta.txt'
@LanaDominkovic Ай бұрын
Hi, it seems your program cannot access following file: sequence.fasta.txt you need to have it on your local machine :)
@fuma9532 5 ай бұрын
At 35:35 I get an import error "ImportError: cannot import name 'GC' from 'Bio.SeqUtils'" I used: from Bio.SeqUtils import gc_fraction gc_fraction(covid_dna) instead
@fuma9532 5 ай бұрын
At 20:11 I ran into an error: "StreamModeError: GenBank files must be opened in text mode." By looking at the documentation, I added retmode="text" to the efetch parameters, that seems to have solved it.
@Oriemu-tw 5 ай бұрын
Hi, I am new in Biopython and I found your channel. Thank you for the informative content! Unfortunately, when I followed the step to use the parse function (SeqIO), it didn't work. I encountered an error: "FileNotFoundError: [Errno 2] No such file or directory: 'ls_orchid.fasta.txt'". However, I checked the examples file in the Biopython package, and the file "ls_orchid.fasta" is there. I have no idea why the error happened. Have you ever encountered this problem?
@Queen-ds1py 3 ай бұрын
This is because you have no file named that.
@itsjs000 5 ай бұрын
Hello, have you ever written a script to do a multiple alignment via ClustalW using biopython?
@betterlife6510 6 ай бұрын
How is bioknformatics jobs in ca
@jorgedeoliveiraecheimberg4522 6 ай бұрын
Hi Lana, I've been attempting to get Homo Sapiens sequences from blastn (nt) by using byopithon. So, I got the transcripts but genomic sequences. Could you send-me a small python script to do that? Many thanks!
@tannerkerby8134 7 ай бұрын
Thank you for uploading these. Really helps learn Biopython while including some insightful information as well.
@jessehines4044 7 ай бұрын
Which code editor for python do you use? Great video BTW, I loved it.
@LanaDominkovic 7 ай бұрын
Hi, I use PyCharm. Thank you for your comment :D I am really glad you loved it
@jessehines4044 7 ай бұрын
@LanaDominkovic Of course, you're welcome your videos are great. Wow pycharm, that's expensive because for the scientific version, they charge 99$/month.
@LanaDominkovic 7 ай бұрын
@@jessehines4044 you dont need professional, download community edition should be enough :) and that one is free
@Nishabled 9 ай бұрын
GREAT JOBS, i'm a bit confuse on how you gor the alignment output of the string(s) and substing/motif(t) ?
@LanaDominkovic 9 ай бұрын
hello can you elaborate on what excatly confuses you to give you more details? thank you :)
@buraqghassanhamza6530 11 ай бұрын
Thanks lana ❤️,it’s work but i have these message BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module. warnings.warn( Can you tell me how can i fix the code depending on this message pls?
@LanaDominkovic 9 ай бұрын
hello. did u try replacing bio.pairwise2 call with Bio.Align.PairwiseAligner call? thank you for nice message
@jonathan.m.phillips 11 ай бұрын
Great video 👍
@LanaDominkovic 9 ай бұрын
Glad you enjoyed it
@velamuriishwarya7100 11 ай бұрын
Thnx a lot!!
@LanaDominkovic 9 ай бұрын
You're welcome!
@ikoks272 Жыл бұрын
what about Germany? How are bioinformatics prospects in Germany?
@datadrivendev Жыл бұрын
What about Canada? Is there interesting opportunities there?
@sapienthought1103 Жыл бұрын
hello thank you just dont stop making content like this
@LanaDominkovic Жыл бұрын
Thank you :)
@mdominac8028 Жыл бұрын
Lost all brain cells watching this.
@nouhoumsanogo6568 Жыл бұрын
thank I really like
@LanaDominkovic Жыл бұрын
I'm glad you like it
@Sholto_David Жыл бұрын
Thanks for uploading this! How long do your responses typically take, I seem to be sat here for several minutes to get a result, is that normal?
@broncioaguilar1757 Жыл бұрын
Really loved your explanation with a Jupyter Notebook! So helpful! Thanks! :)
@LanaDominkovic Жыл бұрын
Glad it was helpful! :)
@GaryMahal Жыл бұрын
this was sooooooooo good :) thank u so much
@LanaDominkovic Жыл бұрын
You're so welcome!
@Alex-gw6pm Жыл бұрын
Thank you very much! very helpful content
@LanaDominkovic Жыл бұрын
You're very welcome!
@Alex-gw6pm Жыл бұрын
@@LanaDominkovic just I would be very grateful if you explain alittle more slowly. Thank you again for your great effort and have a good day!
@jaswanthchotu6068 Жыл бұрын
How was the bioinformatician career in us.can we get jobs over there after Masters?
@LanaDominkovic Жыл бұрын
hello, in the video i show how to search job market in US, you can check on glassdoor current job postings and required experience :) I am sure you can find something with Masters degree
@jaswanthchotu6068 Жыл бұрын
@@LanaDominkovic thanku very much dear
@CaucherIlami Жыл бұрын
Hey Lana, Your channel is awesome. Thanks for sharing such mind catching videos. I've learned Biopython using your tutorials.
@LanaDominkovic Жыл бұрын
Glad you like them!
@CaucherIlami Жыл бұрын
You made life live! thanks for your support. May I have your email id? I have some queries about codes that you run in this tutorial@@LanaDominkovic
@JasperCove Жыл бұрын
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 Жыл бұрын
thank you for nice comment, much appriciated:) can you let me know exact problem? as i understood rosalind doesnt accept your answer or?
@JasperCove Жыл бұрын
@@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 11 ай бұрын
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
@handsome_man69 Жыл бұрын
are there any hot babes in bioinformatics?
@Vishnuram-007 Жыл бұрын
Thank you so much mam . Very clear and beginner friendly explanation.
@LanaDominkovic Жыл бұрын
Most welcome 😊
@ayaqz3144 Жыл бұрын
thank you
@s1va3209 Жыл бұрын
Superb.
@LanaDominkovic Жыл бұрын
Thank you! Cheers!
@mariposa.00 Жыл бұрын
Hello , bioinformatics jobs can freelance ?
@LanaDominkovic Жыл бұрын
Hi, if you advertise your work and services on sites like upwork or fiverr I am sure somebody in need of your expertise will reach you
@faridxacur-lz7hl Жыл бұрын
Can you please provide book references to learn about Omics? Preferably as a learning path , you know , "from zero to hero". -Genomics -Epigenomics -Transcriptomics -Proteomics -Metabolomics I know that this is the kind of question that you can ask in Chat GPT , i got answer from that source but , as a self-taught programmer i can say that , in terms of certain , i mean , "What are you going to get after INVEST YOUR TIME in some course , book or material?" , there is nothing better than the advice of someone who has experience/expertise (to provide context about what im talking about ---> kzbin.info/www/bejne/q6umhXuaopWHlbM).
@comics21nt70 Жыл бұрын
great tutorial!
@LanaDominkovic Жыл бұрын
Thanks!
@somayehghasemi6112 Жыл бұрын
thanks very useful
@LanaDominkovic Жыл бұрын
Glad it was helpful!
@shoebikhlas5784 Жыл бұрын
Hi Lana, really appriciate your efforts. You really explains it very well. I am a bigginer in this feild. I was curious, if we can count number of mutations in each individual sequence of a fasta file (fasta file having multiple sequences) and print out the result " sequence header and corresponding number of mutation detected". In one of my project i have to sort and remove sequences from my fatsa file having mutations more than a set threshold.
@LanaDominkovic Жыл бұрын
Hi, thank you for the nice comment. yes it would be possible to count number of mutation in each individual sequence, you would just need to know delimiter in file which recognises the start of new sequence and when reading file, count sequence by sequence
@Stop-and-listen Жыл бұрын
Would you happen to have an example using blastx?
@vinayakkawale804 Жыл бұрын
thank you mam I am doing bachelor's in bioinformatics and I have no idea what can I do next can you suggest for career-related education best for me
@emilianobalderasramirez8954 Жыл бұрын
Wow! thanks for the tutorial!
@shehryarqureshi8500 Жыл бұрын
How good at genetics do I need to be if i want to study Bioinformatics at masters level? i am currently studying biomedical sciences at undergraduate level and am looking at what to do next, i have struggled with genetics my whole degree. bioinformatics interests me a lot, even tho im terrible at genetics, mainly cus of the computing and statistical/analytical aspect of it. any advice would be greatly appreciated!
@charlesedward4114 2 жыл бұрын
It is very interested to video is abut bioinformatics as I'm the biology & computer science specialist from height school to university in my country so it very very Good Both field Biology & computer science Thanks you for creating the video
@LanaDominkovic Жыл бұрын
Thank you :)
@user-dx7nk6bl9s 2 жыл бұрын
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?...
@MarcosVinicius-qw8pi 2 жыл бұрын
awesome!
@omniatomniah 2 жыл бұрын
the first notebook is deleted
@LanaDominkovic 2 жыл бұрын
day 1 notebook? it's here: github.com/lanacaldarevic/12-days-of-biopython/blob/main/12_days_of_biopython/day_01/day_01-quality_reads_fastq.ipynb
@osos3170 2 жыл бұрын
Thank you for the video. I wanted to ask, can I compare a sequence against a fasta file that I have locally? basically I have 2 fasta files, and I wanted to find hits between them within a certain e value threshold. Is that possible?
@juanfra1997 2 жыл бұрын
after obtaining the protein how do i know wich amino acids are? by the way nice video!