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Results tagged with genbank
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user 3848
NCBI sequence annotation flat file.
1
vote
How to properly annotate sequence variants and errors in a GenBank file format and how to ke...
Genbank, needs a joint agreement with all parties concerned because it is certainly valid information for someone. …
M__♦
- 13k
0
votes
Parsing a genbank file and outputting specific feature information to a csv using BioPython
I've used SARS-CoV-2 (Genbank: PA544053), because there was no Genbank entry given in the OPs question. If my example is representative (might not be) I think its about the object attributes. … Note, I don't know the difference between SeqIO and GenBank objects. …
M__♦
- 13k
1
vote
Accepted
BioPython SeqIO fails with Invalid Alphabet found
Quickly ...
from Bio.Alphabet import generic_protein
from Bio.Seq import Seq
then ..
myprot = Seq('EXAMPLEPROT', alphabet=generic_protein)
M__♦
- 13k
2
votes
Accepted
Why does the Genbank phylogenetic tree of 4000 sars-cov-2 sequences only display 200 nodes?
Okay, I'll provide a formal answer, Genbank phylogeny is to get a gist of the diversity. It isn't a formal phylogenetic analysis. … If you think Genbank is okay, then try MegaX its very point and clicky. Generally, maximum likelihood phylogeny has returned to vogue for at least 1 decade now (previously Bayesian). …
M__♦
- 13k
1
vote
which NCBI tool is optimized to identify a species from a DNA fragment?
The fragment in yellow is the query and the sequence next to it was the sequence already deposited on Genbank of this ancient isolate. …
M__♦
- 13k
-1
votes
How do i search by these gene properties in NCBI's GenBank?
Genbank uses taxon id internally, it's a database reference not a biological code, and can't be used as input - its completely unique to Genbank. … Clarification [taxon id] is not a field in Genbank, it's a database code, the tag is [organism]. …
M__♦
- 13k
1
vote
How to programatically download SARS-CoV-2 fasta from NCBI/Genbank via API?
There are three ways to do this,
If you click on this link Your NCBI examples. Its done.
You would then just click "download"
Click "next", click "next"
The sequence then downloads.
Essentially all …
M__♦
- 13k
1
vote
Accepted
What is the best Query to retrieve DNA from NCBI?
The search term you need is [gene name] rather than [title]. For example,
(Gasterosteus aculeatus[Organism] AND cox1[Gene Name]) OR (Gasterosteus aculeatus[Organism] AND coi[Gene Name])
Results in 2 …
M__♦
- 13k