Can you suggest eukaryotic genome annotation tools which will give the output of my fasta genome in gbk format. My genome is not in NCBI. If I want to add it to the NCBI, do I first need to annotate it in order to download gbk?
thank you for the wonderful videos. I annotated virus genome with prokka and got the outputs. i tried using Artemis following your video, but Artemis can not read .gbk file saying read failed, entry contains no sequence. Any suggestions? With many thanks
Yes you can. This page gives examples of organisms whose genomes has been visualized with artemis: www.sanger.ac.uk/project/artemis-visualising-analysing-and-browsing-next-generation-sequence-data/
@@bioinformaticscoach thank you much!!! I managed to create the DNAplotter but mine does not contain the numbers outside the circle that indicate the size of the genome. Wonder how that can be added (the sequence of the organism Im working with is not in the NCBI)
@@bioinformaticscoach I have both, but the whole genome is in fasta file while the gfk file while is incomplete, I was wondering if there is a way to convert my complete fasta file to genbank file.
To generate such images, the genbank format is required because it uses information such as (feature types, regions,etc) . These information cannot be found in the fasta. In order to generate genbank file , you have to annotate your genome. If I may ask, is your data a bacterial genome ?
Hi, thanks this is very helpful. However, I am encountering problems since I can not distinguish forward and reverse sequence, but I am getting only one circle. Please can you help?
Hiii, i have a little question,How can I use ACT to compare different genomes? I’ve tried but it gives me an error ''while reading from sequence.gb: regulatory is not a valid key''
Genbank files contain features. So you have check to make sure you have regulatory features in our data. For comparison, the question is , what are you comparing. ? No. of genes, sequences,featues, etc.
@@mariadelcarmenmenagaviria721 If comparing sequences, then I will suggest you do some phylogeny analysis.here is a playlist for you : th-cam.com/play/PLe1-kjuYBZ04XNJfGWnVPjx_y1o0O6aJh.html In addition, you can also look at comparing sequence length,GC content,etc. You can write some python scripts to help you do that. here is a playlist that may help : th-cam.com/play/PLe1-kjuYBZ07THLNZtNAyThcl5Qy6NT5J.html You can also generate ring structures using BRIG. Here is a video on that : th-cam.com/video/pobQgE4z-5Q/w-d-xo.html
Thank you so much, very useful your tutorials!!!
How can I add cog annotations to the genome map?
Can you suggest eukaryotic genome annotation tools which will give the output of my fasta genome in gbk format. My genome is not in NCBI.
If I want to add it to the NCBI, do I first need to annotate it in order to download gbk?
thank you for the wonderful videos. I annotated virus genome with prokka and got the outputs. i tried using Artemis following your video, but Artemis can not read .gbk file saying read failed, entry contains no sequence. Any suggestions? With many thanks
Thank you for the video. Please is this applicable to data of different organisms example human?
Yes you can. This page gives examples of organisms whose genomes has been visualized with artemis: www.sanger.ac.uk/project/artemis-visualising-analysing-and-browsing-next-generation-sequence-data/
@@bioinformaticscoach thank you, I will check the page.
@@m.aissah8723 I will making more videos on artemics later on. But in the meantime you can do some exploration yourself.
@@bioinformaticscoach ok, thank you and we shall wait for them
Instead of NCBI, if I have the fast file containing all the information of the genome, can I still achieve the same?
Sure you can. You need the data to be in genbank format. Notice that the example data I used was downloaded from NCBI
@@bioinformaticscoach thank you much!!! I managed to create the DNAplotter but mine does not contain the numbers outside the circle that indicate the size of the genome. Wonder how that can be added (the sequence of the organism Im working with is not in the NCBI)
@@eswinipi Did you use fasta file or genbank (.gbk) ?
@@bioinformaticscoach I have both, but the whole genome is in fasta file while the gfk file while is incomplete, I was wondering if there is a way to convert my complete fasta file to genbank file.
To generate such images, the genbank format is required because it uses information such as (feature types, regions,etc) . These information cannot be found in the fasta. In order to generate genbank file , you have to annotate your genome. If I may ask, is your data a bacterial genome ?
Hi, thanks this is very helpful. However, I am encountering problems since I can not distinguish forward and reverse sequence, but I am getting only one circle. Please can you help?
Are you using the data provided in the tutorial? or you are using your own file?
Hiii, i have a little question,How can I use ACT to compare different genomes? I’ve tried but it gives me an error ''while reading from sequence.gb: regulatory is not a valid key''
Genbank files contain features. So you have check to make sure you have regulatory features in our data. For comparison, the question is , what are you comparing. ? No. of genes, sequences,featues, etc.
@@bioinformaticscoach I’m comparing genes. Genes from the same microorganism isolated from different environments.
Sorry i'm comparing sequences.
@@mariadelcarmenmenagaviria721 If comparing sequences, then I will suggest you do some phylogeny analysis.here is a playlist for you : th-cam.com/play/PLe1-kjuYBZ04XNJfGWnVPjx_y1o0O6aJh.html
In addition, you can also look at comparing sequence length,GC content,etc. You can write some python scripts to help you do that. here is a playlist that may help : th-cam.com/play/PLe1-kjuYBZ07THLNZtNAyThcl5Qy6NT5J.html
You can also generate ring structures using BRIG. Here is a video on that : th-cam.com/video/pobQgE4z-5Q/w-d-xo.html
@@bioinformaticscoach Thanks!!!!!!!!!!!