User: Lille My

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Lille My30
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4 months ago
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2 years, 8 months ago
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Posts by Lille My

<prev • 19 results • page 1 of 2 • next >
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Comment: C: retrieving only one result using entrez direct
... Thanks, but I get a similar error message saying that this is not a valid parameter for esearch. ...
written 4 months ago by Lille My30
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Comment: C: retrieving only one result using entrez direct
... This: esearch -db protein -query rubisco | efetch -retmax 5 -format fasta doesn't work. I get the efetch error message saying that retmax is an unknown option. Thanks! ...
written 4 months ago by Lille My30
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retrieving only one result using entrez direct
... Hi all, I'm retrieving proteins using entrez direct esearch. My search words retrieve many proteins, and I only need the first few results. I could do this with bash, but it takes time to retrieve all the results and I would like to know if there is a way to do it with esearch. esearch -db ...
ncbi edirect written 4 months ago by Lille My30 • updated 4 months ago by vkkodali1.2k
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Using entrez-direct inside a for loop in bash
... I'm trying to retrieve the genome from which a series of proteins are derived. there is more than one assembly for each protein, so I need to create a file where they are linked. I use the following: for id in `cat gi-list-file`; do elink -target nuccore -db protein -id $id | elink - ...
ncbi bash written 6 months ago by Lille My30 • updated 6 months ago by genomax71k
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Comment: C: finding the genome of origin of a protein on genbank
... I'm using the following: epost -input file-with-gi-numbers -db protein | elink -target nuccore -db protein | elink -target assembly | esummary | xtract -pattern AssemblyAccession -element AssemblyAccession I get a list of GCA numbers that is longer than the list of accessions. I would like to ...
written 6 months ago by Lille My30
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Comment: C: finding the genome of origin of a protein on genbank
... Thanks! this works. I'm also trying to have it return the original query prtotein ID. could you also help with that? thanks ...
written 6 months ago by Lille My30
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Comment: A: finding the genome of origin of a protein on genbank
... Thank a lot, it works. Do you know how to do this query in batch? I have a list of ids in a file and at the second attempt there is an error message. ...
written 6 months ago by Lille My30
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Comment: C: finding the genome of origin of a protein on genbank
... Interesting. When I manually checked a few on the website, I found a link through the Identical Protein Groups database. An example is WP_043107373.1, which through some digging is associated with GCF_000801295.1. it also has an NZ number (NZ_AP012978.1), but I think this might be the accession nu ...
written 6 months ago by Lille My30
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Answer: A: Algal vs bacterial 16s chloroplast
... Are you using qiime2? if you are, you can view the sequences using qiime2 viewer (rep-seqs.qzv if you follow the tutorial). from there you can press the link of the relevant sequence and it opens a blast window. If you are not sure which sequence it is, you can look it up in taxonomy.qzv. ...
written 6 months ago by Lille My30
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finding the genome of origin of a protein on genbank
... Hi all, I have a list of protein ids, of the WP_ type. I need to find the assembly (GCA_, GCF_ ) they come from. Any ideas on how to do it? Thanks :-) ...
ncbi assembly written 6 months ago by Lille My30

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Popular Question 2.4 years ago, created a question with more than 1,000 views. For Combining two fasta sequences into one

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