User: dago
dago • 2.2k
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Posts by dago
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Comment:
C: Multiple ORF's of same length
... I think what you need is not really clear. Can you provide more details, please. ...
written 7 hours ago by
dago • 2.2k
0
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1
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143
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1
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... Hi, thank you very much for the answer!
You are right! Adding `if f.type == "CDS"` fixed it! ...
written 1 day ago by
dago • 2.2k
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143
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... I checked the gbk, it looks fine. I will try twitter..:) ...
written 1 day ago by
dago • 2.2k
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1
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143
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1
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... ok, I am officially confused. If I run:
for i in record_dict:
for f in record_dict[i].features:
print f.qualifiers.keys()
I get
['locus_tag', 'inference', 'codon_start', 'product', 'transl_table', 'translation', 'protein_id']
['locus_tag']
['locus_tag', 'inference', 'c ...
written 1 day ago by
dago • 2.2k
1
vote
1
answer
143
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... I thought the same, but when I check the keys locus_tag is in there:
['locus_tag', 'gene']
['locus_tag', 'inference', 'codon_start', 'EC_number', 'transl_table', 'product', 'translation', 'gene', 'protein_id'] ...
written 1 day ago by
dago • 2.2k
10
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143
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answer
... I have a gbk of a draft bacterial genomes (meaning multiple contigs).
I want to extract some info about specific genes, and I get an error I cannot understand.
Parse the gbk
record_dict = SeqIO.to_dict(SeqIO.parse("SpeciesA.gbk", "genbank"))
My file looks:
for i in record_dict:
...
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... I am not familiar with the program you are using. But if the result of the analysis are contigs, I guess as a product of a whole genome alignment, I would say that in 99.9% of the case you will have multiple genes on them. Therefore you would need to do 2 things: gene calling and annotation(if neede ...
written 5 weeks ago by
dago • 2.2k
0
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2
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280
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2
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Comment:
C: Bacterial de novo genome assembly
... Look these:
https://www.biostars.org/p/120386/
And also a list of tools available is [here][1]. You can check the one that work in windows amongst them.
[1]: https://omictools.com/genome-assembly-category ...
written 7 weeks ago by
dago • 2.2k
1
vote
2
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280
views
2
answers
Comment:
C: Bacterial de novo genome assembly
... check assembly quality with [QUAST][1]
[1]: http://bioinf.spbau.ru/quast ...
written 7 weeks ago by
dago • 2.2k
0
votes
2
answers
280
views
2
answers
Comment:
C: De novo genome assembly
... what did you try? There are plenty of tutorials out there. What organism do you have? Bacteria? ...
written 7 weeks ago by
dago • 2.2k
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