Questions tagged [entrez]

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Converting Gene Symbol to Entrez ID in R

I analyzed a GEO dataset and found 99 DEG.Now I want to analyze functional enrichment analysis and for that reason I have to convert my gene symbol to entrez id.But I cannot do that,I tried but my ...
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1 vote
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19 views

Download COX1 (COI) gene via biopython using accessions for entire mitochondrial genomes

I have a list of accessions for the the entire mitochondrial genomes for big cats. I need to download the COX1 genes for each of these accessions. Here is one accession and here is a link to its COX1 ...
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1 vote
1 answer
37 views

Getting translation table of organisms through Entrez direct (or other CLIs)

I have a long list of NCBI taxonomic ids for organisms and I want to write a script to get their corresponding translation tables. Is there a way to do this through Entrez? (packages in R, Python etc. ...
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1 answer
2k views

curl: (22) The requested URL returned error: 400 Bad Request when using entrez direct

I've just dowloaded entrez direct on my Mac and I was trying to perform some simple queries like: ...
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1 vote
1 answer
275 views

Convert Entrez gene ids and HUGO symbols, whose genome assembly is unknown, to GRCh38 Ensembl gene ids

I want to use a file available on a database called DepMap (https://depmap.org/portal/download/). This file called ...
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1 vote
1 answer
127 views

Entrez (Biopython) esearch and efetch not returning sequence as expected

I'm trying to use Entrez (through Biopython) to download the sequence of a TMV replicase gene. I have the following code: ...
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1 vote
2 answers
46 views

Long-form gene summary

The following (thx to these answers) retrieves the info, in particular a long summary (such as "The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding ...
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  • 151
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1 answer
396 views

Using Entrez.efetch() to retrive .fasta file from any NCBI database?

I tried to use these python codes to retrieve a .fasta file from gene database, but the output were the parameters of the report ...
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3 votes
2 answers
158 views

How to obtain NCBI Nucleotide (Entrez) IDs for all E coli sequences?

I would like to gather a list of ALL E coli NCBI (Entrez/Nucleotide) IDs so that I can download fna and faa files, through a function like this: ...
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1 vote
0 answers
23 views

Finding annotated counterpart after BLASTn with efetch (Biopython)

I am creating a pipeline for the identification of unknown transcripts. After a local BLASTn search of the transcripts, I have a large list of the respective hits with different genomes. I have the ...
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  • 26
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1 answer
37 views

Why doesn't an (Entrez eutils) einfo request for "gene" return the link gene_nucleotide or gene_nucleotide_pos links?

I'm updating a galaxy tool wrapper for Entrez's eutils suite and I'm trying to create a form with valid link selections (among other things) based on the "from" & "to" ...
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  • 189
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1 answer
40 views

How to extract metadata from NCBI's experiment?

I want to extract metadata from experiment SRX1596422. I have sratoolkit and Entrex direct but not sure what line of code to use. Here's the link for the experiment: experiment SRX1596422
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3 votes
1 answer
85 views

How to query NCBI (Nucleotide database) by a feature qualifier?

I cannot seem to find a way to query nucleotide database (https://www.ncbi.nlm.nih.gov/nuccore) by a specific qualifier of the feature. For example, by /host under the feature "source". For example, ...
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  • 33
1 vote
2 answers
59 views

Why the gene symbol aliases have significantly different sequences?

"Aliases" or "Synonyms" should represent the same gene but with different names. But when I try to find the sequence of one alias and try to match with another alias they are ...
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  • 35
1 vote
1 answer
61 views

rentrez to retrieve NIH files

I'm trying to use rentrez package to retrieve NIH files, and ran the following code (I followed what was on the rentrez tutorial): ...
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4 votes
2 answers
336 views

Entrez.efetch returns incomplete genbank records

I am using the biopython Entrez.efetch command to retrieve all features (CDS, mRNA, ...) of some genomes. In this case (NC_014649, Acanthamoeba polyphaga mimivirus), it works as expected: ...
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  • 595