User: dago

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dago2.2k
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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 dago2.2k
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Comment: C: Biopython: work with loops and qualifiers from multiple records
... Hi, thank you very much for the answer! You are right! Adding `if f.type == "CDS"` fixed it! ...
written 1 day ago by dago2.2k
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Comment: C: Biopython: work with loops and qualifiers from multiple records
... I checked the gbk, it looks fine. I will try twitter..:) ...
written 1 day ago by dago2.2k
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Comment: C: Biopython: extract qualifiers from multiple records
... 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 dago2.2k
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Comment: C: Biopython: extract qualifiers from multiple records
... 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 dago2.2k
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Biopython: work with loops and qualifiers from multiple records
... 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: ...
genome python biopython gene software error written 1 day ago by dago2.2k • updated 1 day ago by Peter5.5k
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Answer: A: Identifying core proteins -Pangenome
... 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 dago2.2k
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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 dago2.2k
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Comment: C: Bacterial de novo genome assembly
... check assembly quality with [QUAST][1] [1]: http://bioinf.spbau.ru/quast ...
written 7 weeks ago by dago2.2k
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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 dago2.2k

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