User: Solowars

gravatar for Solowars
Solowars50
Reputation:
50
Status:
New User
Location:
Brazil/Porto Alegre/UFRGS
Last seen:
13 hours ago
Joined:
1 year, 6 months ago
Email:
g*******@gmail.com

Posts by Solowars

<prev • 26 results • page 1 of 3 • next >
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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 7 days 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 7 days 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 7 days 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 7 days ago by Solowars50
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Comment: C: Deprecated identifiers in Ensembl?
... Thanks a lot for your help! ...
written 8 months ago by Solowars50
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Comment: C: Deprecated identifiers in Ensembl?
... Thanks a lot for your help! Best ...
written 8 months ago by Solowars50
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Comment: C: Deprecated identifiers in Ensembl?
... Sure! Please consider these examples: ENSMICG00000011090 ENSMICG00000011081 ENSMICG00000011093 ENSDORG00000003549 ...
written 8 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 8 months ago by Solowars50 • updated 8 months ago by Emily_Ensembl18k
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Comment: C: Best way to identify proteins within a family?
... Well, let's say that we have a big receptor family, like GPCRs, which contains receptors for a broad array of neurotransmitters. However, I'm interested in a specific subgroup (receptors of a specific neurotransmitter), and these receptors don't have a specific domain characterizing them, other than ...
written 13 months ago by Solowars50
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Best way to identify proteins within a family?
... Dear community, I'm interested in retrieving deep homologies for a number of genes that belong to a protein superfamily (let's say, GPCR). For it, one of the strategies was to perform HMMER searches, using an alignment or a HMM created from an aligment. For what I have read, many people use specif ...
domain orthologs oma homology hmmer written 13 months ago by Solowars50

Latest awards to Solowars

Scholar 7 days ago, created an answer that has been accepted. For A: HTTP 400: Bad request error in Biopython Entrez.efetch
Supporter 14 months ago, voted at least 25 times.

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