Questions tagged [ncbi]

Use this tag to refer to the questions related to NCBI

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1 vote
0 answers
19 views

segmasker doubles found intervals

During NCBI BLAST+ segmasker output exploration, I found out that for some sequences, the program returns the same interval twice: ...
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2 votes
0 answers
26 views

Why does segmasker modify headers?

When parsing NCBI BLAST+ segmasker output, I realized the program modifies almost every header containing these strings: ( or )...
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2 votes
2 answers
81 views

How to wget a gff from NCBI database?

Say I want to use wget to download a gff file for the X chromosome of release 5.57 of the Drosophila melanogaster genome. The NCBI page with the gff file for just this is here. However, I do not see ...
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1 vote
1 answer
70 views

How to get full headers with tabs as separators with segmasker?

I try to pass a .fasta file with headers where tabs are used as separators as input file to NCBI BLAST+ segmasker: ...
  • 185
1 vote
1 answer
21 views

Retrieval protein definition from accession ID

I have a list of protein accessions: XP_025107904.1 PVD22034.1 AJA37836.1 How can I obtain the definition of the protein, and the related organism? Output: ...
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4 votes
1 answer
45 views

How to promote assemblies into genomes in NCBI?

Note: I've never submitted an assembly/genome to NCBI, so excuse if my perspective is flawed. I'm working with Drosophila subobscura. (spring fruit fly) I see here https://www.ncbi.nlm.nih.gov/data-...
1 vote
1 answer
52 views

Fixing FASTA file for Local BLAST Database

I recently prefetched 157 SRA files from an NCBI BioProject using the SRAtoolkit. I then used the toolkit to download those files in FASTA format. Each individual FASTA file looks something like this: ...
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1 vote
1 answer
24 views

CLI access to genomes/proteomes by BioSample ID [duplicate]

This question was also asked on Biostars I'd like to download multiple genome assemblies or proteomes using a set of BioSample IDs from NCBI. I'm able to find the assemblies belonging to the BioSample ...
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3 votes
0 answers
28 views

How are BLAST record scores calculated in biopython

Can someone explain how the score is calculated for Bio.Blast.Record.Description? For example, if Record.Description.num_alignments is >1, is ...
4 votes
2 answers
91 views

Downloading genomic protein files from accessions in Python

I am trying to download the _protein.faa.gz files for genomes given their accession numbers through Python. Ideally, I would like to do this without third party ...
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2 votes
1 answer
28 views

How good does the assembly of an NCBI prokaryotic genome have to be in order to argue gene loss?

NCBI has several labels for assembly completeness - Complete, Scaffold, Chromosome and Contig. Complete would be a circularized genome (or linear, rarely) For a Complete genome it's fairly ...
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2 votes
2 answers
168 views

Elegant Way to Extract Gene Symbols from FASTA Headers

I've downloaded the RefSeq transcript sequences (FASTA format) for the GRC38 patch 14 build of the human genome and would now like to extract the gene symbols (only) in order from the headers. I'm ...
3 votes
2 answers
79 views

How can I download from NCBI all the ITS genes and the related taxonomy?

I would like to download all the ITS1 and ITS2 genes from NCBI in a fasta file. And, I'd like to download even the related taxonomy of each sequence. Thanks, Marco
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0 votes
1 answer
49 views

How can I get data of single cell RNA sequence with raw count?

I am using dataset GSE85241, but I can't find the read counts of the dataset. It only provides with RPKM values. How can I find the read counts of a dataset?
3 votes
1 answer
71 views

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
131 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 ...
0 votes
1 answer
62 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 ...
3 votes
2 answers
93 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 ...
2 votes
2 answers
46 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 ...
0 votes
0 answers
94 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 votes
0 answers
12 views

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: ...
1 vote
1 answer
45 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. ...
1 vote
0 answers
52 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 ...
1 vote
0 answers
30 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
23 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, ...
-1 votes
1 answer
151 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 ...
2 votes
1 answer
111 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
47 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....
1 vote
1 answer
279 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
343 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 ...
4 votes
1 answer
287 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: ...
1 vote
0 answers
18 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 ...
1 vote
2 answers
48 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
85 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
65 views

Convert .smp downloaded from NCBI CDD into HMM(.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 ...
0 votes
1 answer
697 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 ...
2 votes
2 answers
731 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
201 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: ...
1 vote
0 answers
132 views

How to read E-value annotation on NCBI BLAST?

I am seeking clarification on how to read the E value annotation on NCBI's BLAST results. What I understand so far: E -values are the expected value of the number ...
0 votes
2 answers
65 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&...
6 votes
1 answer
90 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 ...
3 votes
1 answer
108 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
65 views

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 ...
1 vote
1 answer
33 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?
3 votes
1 answer
118 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 ...
0 votes
1 answer
107 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 ...
0 votes
1 answer
34 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: ...
0 votes
1 answer
177 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 ...
  • 1,417
0 votes
1 answer
53 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 ...
3 votes
2 answers
318 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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