User: Lille My

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

<prev • 16 results • page 1 of 2 • next >
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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 8 days ago by Lille My30 • updated 8 days ago by genomax64k
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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 8 days 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 8 days 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 9 days 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 10 days 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 10 days 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 10 days ago by Lille My30
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comparing phylogenetic trees
... I have two trees. I want to compare them to a third tree, to see which of the two is more similar to the third one. is there an easy way to do it? thanks! ...
phylogeny ml raxml written 23 months ago by Lille My30 • updated 23 months ago by agoel30
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Comment: C: splitting bootstrapping analysis in raxml
... So, if I perform the analysis as a two step process, first searching for the best tree and then doing the bootstraps? Do you by any chance remember the options to use? ...
written 2.1 years ago by Lille My30
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splitting bootstrapping analysis in raxml
... I would like to construct a very large tree using raxml. Last time I ran raxml on the data the server had to reboot and all data was lost. Is there a way to conduct the analysis step by step, saving all of the trees along the way? thanks! ...
phylogeny bootstrapping raxml written 2.1 years ago by Lille My30 • updated 2.1 years ago by h.mon24k

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Popular Question 23 months ago, created a question with more than 1,000 views. For Combining two fasta sequences into one

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