Questions tagged [ncbi]

Use this tag to refer to the questions related to NCBI

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What does this accession NCBI code mean: 6MWN_B?

According to this article, accession codes should consist from a combination of uppercase letters following a combination of digits. If this is a RefSeq, it can have a prefix as a combination of ...
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2 votes
3 answers
83 views

How to programatically download SARS-CoV-2 fasta from NCBI/Genbank via API?

I would like to download a number of SARS-CoV-2 fastas from NCBI/Genbank using a web endpoint. I looked on their website but it's confusing. I have the accession numbers, but can't figure out how to ...
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0 votes
1 answer
53 views

How to solve correlation problems between different samples in scRNA-seq?

I am trying to align and merge different samples from NCBI. I end up having correlation problem with these sample. The picture below shows an heatmap of the R² by doing a linear regression between 2 ...
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3 votes
2 answers
82 views

How to get the number of complete phage genomes available on ncbi?

I am looking to establish the total number of complete phage genomes available on NCBI. I am not looking for any specific type, but want to understand the total diversity available. How can I perform ...
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2 votes
2 answers
44 views

Is there a publication database or search engine offering geneID or UniProtID correlation?

Do we have a publication database or search engine that offers geneID or UniProtID correlation? For example, I search "IPS cells" -> I want to know what genes or proteins are under active ...
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0 votes
0 answers
34 views

How to download metadata in SRA (i.e., SraRunTable.txt) using Unix commands?

We can obtain metadata (the SraRunTable.txt file) from the webpages in SRA. How to get this file using Unix commands? A potential solution was given in https://bioinformatics.stackexchange.com/a/...
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0 answers
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xtract from eutilities not exctracting the information I need

I'm running the following command which uses the NCBI e-utilities: esearch -db bioproject -query "PRJNA198476 [PRJA]" | esummary This returns: ...
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1 vote
1 answer
36 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 vote
0 answers
30 views

Downloading exon-wise gene sequence using commandline

I want to download exon-wise gene sequence of around 200 genes from NCBI. Is there anyway to do this from terminal? I have the transcript id for each sequence and I am using efetch command to download ...
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1 vote
0 answers
24 views

Tool that can sort NCBI taxonomy ids based on phylogeny

I have a set of NCBI txids (of varying ranks) that I want to sort in some way (e.g. a table or a tree, the way it is sorted isn't super important), based on the current NCBI data for phylogenetic ...
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0 votes
1 answer
20 views

How do you search for new enzymes that are more stable for handling, immobilization?

Noob here. I get that I should deduce what characteristics the ideal new enzyme should meet, and then use tools such as PDB and blast to compare to the old enzymes, and use other tools such as pymol, ...
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-1 votes
1 answer
118 views

How to get a FASTA format file with the DNA sequences of all annotated genes?

I am analysing Pyrococcus Furiosus DNA sequencing data by considering data published here in NCBI. When I click on "Send to">"Gene Features">"FASTA format" I ...
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2 votes
1 answer
55 views

dbSNP GRch37 Download

I am still new to this. I am trying to download the GRch37 dbSNP data from the NCBI dbSNP Browser using the "Send to:" button. But whenever I select "Send to:" > "File"...
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3 votes
2 answers
37 views

Retrieval of metadata of a batch of 3953 sequence data from GISAID database

I need to retrieve COVID-19 metadata (such as date of collection of sequence data, location, etc.) for a batch of 3953 GISAID accessions from the GISAID database. I am not very comfortable with GISAID....
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1 vote
1 answer
120 views

Downloading PSSM file from NCBI PSI-Blast results after the UI update

It used to be easy to download off a results page of a PSI-Blast from NCBI the PSSM (scorematrix). Now I cannot seem to find an asn file that is a scorematrix —<...
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1 vote
2 answers
120 views

How to identify the DNA sequence of a gene in the complete genome sequence FASTA format file?

I need to identify the sequence of a gene in the complete genome sequence . I thought it was simple, instead it is not a straightforward task ! My method was the following: I downloaded the FASTA ...
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4 votes
1 answer
124 views

Programmatically retrieve Metadata from SRA Run Selector

I previously asked a question about how to retrieve the Accession List associated with a SRA project. The answer was: ...
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1 vote
0 answers
16 views

How to interpret complete genome sequence in NCBI

I have a very basic and quick question: does the complete sequence of nucleotides of an organism (for example this one that I am considering in my homework of Pyrococcus Fuoriosus) reported in NCBI ...
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1 vote
2 answers
44 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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1 vote
0 answers
38 views

Convert genbank file into tbl file [closed]

I want to submit some phage sequences to NCBI. So I want to transform a genbank file into a tbl file. Can someone help me please? Thanks
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3 votes
0 answers
50 views

Convert .smp from CDD into HMM file [closed]

Is there a method or tool to convert a .smp file from CDD (Protein Domain File) into a HMM file? I downloaded the CDD files from the FTP site and am more familiar with domain searching with the HMMer ...
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0 votes
1 answer
333 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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2 votes
2 answers
404 views

Timeout when downloading the ncbi nr blast database

I am experiencing timeout problems when downloading the NCBI nr preformatted blast database using the update_blastdb script (version 504861). I run the script with the following paramters ...
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3 votes
2 answers
151 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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0 votes
0 answers
65 views

How to read E-value annotation on NCBI BLAST?

i am a bit confused how to read the current E value annotation on NCBI BLAST results. I looked into the matter but could not find an factual answer . What i understood so far: E -values are the ...
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0 votes
2 answers
43 views

Getting Unique Identifier List for GEO Datasets NCBI

AIM: Download "Unique Identifier List" for the following query from GEO DataSets. Query: ("Expression profiling by high throughput sequencing"[DataSet Type] AND ("Homo sapiens&...
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6 votes
1 answer
75 views

How to search for high coverage SRA entries

The Question I want to find high coverage SRA entries, e.g., above 100x. I guess the best way is to use https://www.ncbi.nlm.nih.gov/sra with an appropriate search term. I don't mind if the search ...
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2 votes
1 answer
53 views

What does the 'suppressed' folder mean on the NCBI ftp genomes website?

I wish to understand the term suppressed in folder nomenclature on the NCBI ftp genomes website? Example: here ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/...
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1 vote
0 answers
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How to deal with the mismatches between gene names obtained from different sources?

For most of the time, I rely on gene ids to combine different datasets. However, in some instances, I have to combine datasets based on gene names. Then, if I don't know the source of gene names in ...
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1 vote
1 answer
30 views

Mapping protein refseq to Gene ID

I have a protein refseq (eg, NP_000029). How can I get the corresponding gene ID (ag, APC) from NCBI using an R package?
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3 votes
1 answer
87 views

How to find all WGS assemblies accessions of a species

Some background Similar to the OP of https://www.biostars.org/p/377840/, I would like to programmatically BLAST a sequence to a local database of all WGS assemblies. Since this isn't feasible for the ...
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0 votes
1 answer
75 views

Get list of urls of GSM data set of a GSE set

I have this GSE dataset ( GSE104279 ) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE104279). I want to make a table with set IDs and ftp urls to use it as a table in galaxy.org I know that we ...
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0 votes
1 answer
31 views

Error while using E-utilities on slurm HPC

I keep getting the error while using E-utilities on Slurm HPC, could you suggest how I can resolve it? SCRIPT: ...
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0 votes
1 answer
131 views

Does NCBI's blast API block my IP?

I am trying to run a blatn command from both my laptop and within a google colab notebook. I am not sure why, but this command runs properly once and then, on the ...
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0 votes
1 answer
34 views

Extracting all information about a sample when using xtract from e-utilities

I would like to extract all information about each SAMPLE after running the following query (run the query and add a ...
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3 votes
2 answers
170 views

How to retrieve the DNA sequence from a particular species and region through command line?

I am new to working with the NCBI database so I am not sure how trivial this question is. I wanted to get DNA sequence of a specific version of the Xenopus tropicalis genome of a specific region (ie 1-...
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0 votes
1 answer
39 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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1 vote
2 answers
89 views

Too many requests error when querying NCBI

I keep getting a "too many requests error" when querying the NCBI SRA database, even though I'm running less than 10 requests per second, and I have an API key, which supposedly should allow ...
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2 votes
1 answer
71 views

Programmatically retrieve Accession List from NCBI

I would like to programmatically retrieve the file "Accession List" from an NCBI page. I'm running firefox, so I'm clicking the file and clicking Ctrl + <...
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0 votes
1 answer
63 views

e-utils api: get chromosome position for each snp on a gene

So I have the following e-utils api-link: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=snp&id=5726&retmode=json it returns all the SNP-ids for the gene with ...
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1 vote
1 answer
48 views

BWA: Detecting Variation between Reference Genome and Short-Read Sequences

I need to identify all loci in the short-read sequence at which the number of microsatellite repeats (i.e. number of copies of "AA," "GTC," etc.) differ from the reference genome, ...
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3 votes
2 answers
877 views

How can I obtain a list of all NCBI gene ID's along with their full name, symbol, and also known as symbols?

I would like to do two things: (1) Obtain a list of all NCBI (Entrez) gene ID's. (2) Obtain the "Official Symbol", "Official Full Name", and "Also known as" fields from ...
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0 answers
22 views

Generating taxonomic hierarchy by species/genus name

I am attempting to create a reference library of DNA plant barcodes in the ITS2 barcode region for plants from a specific region (Panama). I downloaded all the sequences for plants that resulted in a ...
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0 votes
1 answer
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Determine if an organism is microbic or unicellular

I am doing some metagenomic analysis of samples which can only contain microbes due to the experimental setup. For this, it would be useful to be able to distinguish whether a specific organism is a ...
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1 vote
0 answers
20 views

mining DNA barcodes from Genebank/BOLD per location

Is there a method to download all the sequences for a particular geographic region (Panama) for 'DNA barcode' sequences (ITS2, rbcL or trnL). Hopefully, the specimen collection location will include ...
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0 votes
0 answers
29 views

How do I generate a list of post-synaptic gene markers that will guide me in my search for these markers in intestinal stem cells?

I would like to generate a list of gene markers that represent post-synaptic related genes. I will then use this list to search through single cell sequencing data, in order to assess whether certain ...
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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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1 vote
0 answers
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How to (efficiently) search nuccore to retrieve only annotated sequences?

I wish to efficiently search nuccore to retrieve only annotated sequences. By "annotated" I mean that the nuccore entry contains annotation information. An equivalent definition (if I understand ...
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1 vote
0 answers
34 views

Is there a built-in parser for the textual feature table that Entrez.efetch returns?

Entrez.efetch helpfully gives me the feature table of a nuccore entry. If I understand correctly, efetch can only return the ...
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1 vote
3 answers
151 views

Primer-Blast Custom Database [error]

I'm using Primer-Blast to compare a PCR template against a custom database of reference sequences, using Primer-Blast's Custom database functionality. However whenever I try to upload a FASTA file as ...
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