User: Solowars

gravatar for Solowars
Solowars50
Reputation:
50
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Trusted
Location:
Brazil/Porto Alegre/UFRGS
Last seen:
2 weeks, 4 days ago
Joined:
1 year, 10 months ago
Email:
g*******@gmail.com

Posts by Solowars

<prev • 28 results • page 1 of 3 • next >
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Answer: A: How to obtain the chromosome out of an accession number?
... Perhaps you could do it in R, using `rentrez` package. Take a look [here][1]. I'm doing something kinda similar, and it is possible to input those identifiers and ask for a summary (using `entrez_summary` function). In that summary should appear chromosome number/name. Let me know if you need some ...
written 3 months ago by Solowars50
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How to extract all annotations in a genomic range from NCBI using R?
... Hello all, I want to study the genes in the neighbourhood of a number of genes of interest across multiple species. For several reasons, I chose to use NCBI annotations for this task, and I'm playing around with R and dedicated packages, such as `rentrez`, which can achieve many cool things. Howe ...
ncbi R comparative genomics rentrez synteny written 3 months ago by Solowars50
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Answer: A: HTTP 400: Bad request error in Biopython Entrez.efetch
... Ok, I found a solution (KUDOS to genomax for inspiring it). Apparently the problem was indeed in the db parameter 'nuccore'. I switched it to 'protein' and it worked just right! Thank you all for your time and attention. ...
written 4 months ago by Solowars50
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Comment: C: HTTP 400: Bad request error in Biopython Entrez.efetch
... Hi Carambakaracho, I tried to do it via browser, following several examples in the docs, and they worked. However, using my example ids didn't work. I suspect that there must be something related to using 'nuccore' in combination with XP/NP ids...It shouldn't be that, because it worked just right sh ...
written 4 months ago by Solowars50
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Comment: C: HTTP 400: Bad request error in Biopython Entrez.efetch
... Dear genomax. I already signed for an API key, and I run other scripts (in R, though) taking your point into consideration. However, in my example there are no for loops, and as far as I know it would count as a single request, right? If that is the case, there must be something else... ...
written 4 months ago by Solowars50
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HTTP 400: Bad request error in Biopython Entrez.efetch
... Dear all, I wrote a script to retrieve the corresponding nucleotide CDS sequences from a list of protein identifiers from NCBI, using Entrez.efetch in Python 3.7, Anaconda 3, and This script worked well a few weeks ago, but now for some reason it doesn't. Let me show you the code ids=['XP_021 ...
ncbi python biopython entrez sequences written 4 months ago by Solowars50
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Comment: C: Deprecated identifiers in Ensembl?
... Thanks a lot for your help! ...
written 12 months ago by Solowars50
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Comment: C: Deprecated identifiers in Ensembl?
... Thanks a lot for your help! Best ...
written 12 months ago by Solowars50
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Comment: C: Deprecated identifiers in Ensembl?
... Sure! Please consider these examples: ENSMICG00000011090 ENSMICG00000011081 ENSMICG00000011093 ENSDORG00000003549 ...
written 12 months ago by Solowars50
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Deprecated identifiers in Ensembl?
... Dear community, I am working with a gene family across a wide range of chordate species, and one of the steps was to retrieve potential homologs from Ensembl. Interestingly, there were some of these genes that had their ID deprecated in newer versions of Ensembl. However, annotated sequences from t ...
orthologs ensembl annotation written 12 months ago by Solowars50 • updated 12 months ago by Emily_Ensembl19k

Latest awards to Solowars

Scholar 4 months ago, created an answer that has been accepted. For A: HTTP 400: Bad request error in Biopython Entrez.efetch
Supporter 18 months ago, voted at least 25 times.

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