User: tlorin

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tlorin240
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240
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Location:
Switzerland
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4 weeks ago
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3 years, 5 months ago
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t***************@orange.fr

Posts by tlorin

<prev • 65 results • page 1 of 7 • next >
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Comment: C: Get number of available genomes per taxon - NCBI
... @genomax That's true, thanks for mentioning this. For a list of "complete or usable" genomes, what would you suggest instead? ...
written 10 weeks ago by tlorin240
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Answer: A: Get number of available genomes per taxon - NCBI
... I found a way. Count the number of available **genomes** for a given taxon (here, arthropods; note the *wgs*): ``` w3m -dump https://www.ncbi.nlm.nih.gov/nuccore/?term=wgs-master+%5Bprop%5D+AND+arthropoda+%5Borgn%5D|grep "Items:"|rev|cut -f1 -d" "|rev ``` Count the number of available **transcrip ...
written 10 weeks ago by tlorin240
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Comment: C: Get number of available genomes per taxon - NCBI
... OK so there is no direct way to get the number of genomes for any given taxa based on this file: it has to be at the species level. ...
written 10 weeks ago by tlorin240
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Comment: C: Get number of available genomes per taxon - NCBI
... @cpad0112 thank you for your help. What is this line doing exactly? I cannot get the number of available genomes for Arthropoda for instance. ...
written 10 weeks ago by tlorin240
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Comment: C: Get number of available genomes per taxon - NCBI
... 20 only? This does not seem a lot to me (there are already more than 20 drosophila species that are sequenced) ...
written 10 weeks ago by tlorin240
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Comment: C: Get number of available genomes per taxon - NCBI
... @genomax thanks! If I understand correctly, in this file each line corresponds to one species. How would I count for any taxonomic level (say, "Arthropoda" = taxon ID 6656)? ...
written 10 weeks ago by tlorin240
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Get number of available genomes per taxon - NCBI
... Dear all, I am blasting (tblastn) a protein onto WGS on NCBI to search directly into the genomes of some taxa. The protein is not present in every genome and I would like to be able to say "Protein X is present in *n* organisms out of the *N* in this lineage." (so, to be able to count *N*, the to ...
ncbi genome written 10 weeks ago by tlorin240
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Comment: C: Fungi genomes: which database should I use?
... Indeed it's not very easy to access this data. > You could extract all sequences assigned a fungal TaxID (4751) and > blast against those sequences. Could you elaborate on this? Do you mean in NCBI? Thanks! ...
written 4 months ago by tlorin240
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Comment: C: Fungi genomes: which database should I use?
... (By the way, I have found the web interface of JGI to be VERY slow when blasting on the whole fungi lineage.) ...
written 4 months ago by tlorin240
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Fungi genomes: which database should I use?
... Hello, I don't work on fungi - at all. However, it happens that I have to dive into this lineage to understand the evolution of a gene that I thought would be specific to animals, but is not. I have found many resources that seem to harbor genomic resources on fungi. I can think of the [JGI portal ...
genome ensembl jgi fungi blast written 4 months ago by tlorin240 • updated 3 months ago by Biostar ♦♦ 20

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