User: kA

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kA0
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Posts by kA

<prev • 7 results • page 1 of 1 • next >
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How to use extractfeat in bash to obtain feature tags values ?
... Hi, I am writing a bash script to extract some features like CDS from my sequences. I have noticed some of them have tags like Organism and Organelle, whose values I would like to extract. [Like this example of a gene][1] I am not sure what the syntax would be in bash if this is possible, as I ca ...
emboss bash written 8 weeks ago by kA0 • updated 8 weeks ago by Pierre Lindenbaum122k
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Comment: C: How to get nuclear and mitochondrial gene sequences ?
... No I haven't. Although I should specify that I am trying to write a bash script program which would work for eukaryotes in general and not just C. elegans specifically. If I can still do that for other organisms, would my bash script be able to download the sequences from the database ? ...
written 8 weeks ago by kA0
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Comment: C: How to get nuclear and mitochondrial gene sequences ?
... Thanks for the suggestion. Would I be able to do this without installing Entrezdirect ? I would like to use the esearch/efetch utilities as is, with the wget command in bash if possible ? Currently I have something like this: wget "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db ...
written 8 weeks ago by kA0
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Answer: A: How to use extractfeat to get coding sequences?
... I managed to fix it. I was accidentally using FASTA formatted files instead of Genbank flat file format which was a problem. ...
written 8 weeks ago by kA0
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Comment: C: How to get nuclear and mitochondrial gene sequences ?
... Hi, I've added a specific example if that helps. ...
written 8 weeks ago by kA0
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How to use extractfeat to get coding sequences?
... Hi, I am trying to get the CDS of a sequence using extractfeat on bash linux. It gives me the error: Warning: No sequences written to output file I am unsure if my syntax is right, but this is what I have: extractfeat inputFile outputFile -type CDS ...
extractfeat linux bash sequence emboss written 9 weeks ago by kA0
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How to get nuclear and mitochondrial gene sequences ?
... Hi, As part of a script that i'm writing, I need to get the sequence of any desired mitochondrial and nuclear gene of a species from genbank. I'm not sure how to optimise my search and which NCBI databases (genome, gene, nucleotide) would be the best to ensure that I am indeed downloading the corr ...
ncbi sequence mitochondrial genes written 9 weeks ago by kA0 • updated 8 weeks ago by genomax70k

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