Questions tagged [ncbi]

Use this tag to refer to the questions related to NCBI

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16 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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25 views
+50

Convert .smp from CDD into HMM file

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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1answer
23 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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2answers
46 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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7 views

Is there a way to know whether the genome in the NCBI genome database is from type strain?

Is there a method to check whether 1000 genomes downloaded from the NCBI genome database are from type strains? Best regards, Yanpeng Chen
3
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2answers
81 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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0answers
32 views

What is the best practice for gene tree - species tree reconcilation?

when you have a gene tree and you reconcile this with a species tree, how important is it to consider multiple forms of species trees? Does it suffice, to use (e.g.) NCBI species tree ? What is the ...
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0answers
22 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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2answers
38 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
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1answer
60 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 ...
2
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1answer
35 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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0answers
39 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 ...
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1answer
24 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
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1answer
50 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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1answer
29 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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1answer
26 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
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1answer
55 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 ...
0
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1answer
21 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
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2answers
86 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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1answer
24 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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0answers
11 views

How can I specify the experiment type when querying GEO using efilter?

I would like to filter the results I obtain from GEO using the E-utility efilter by Experiment Type (in particular I only want "Expression profiling by high ...
1
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2answers
55 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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1answer
26 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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1answer
20 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 ...
1
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1answer
42 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, ...
3
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2answers
130 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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0answers
29 views

Command-line blastn not responding; trace says “Resource not available”

I hadn't used the NCBI command-line tools for a while, and just got back into it. But no matter where or how I run blastn now, I get an almost complete lack of response: just the initial "BLASTN ...
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0answers
20 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 ...
0
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1answer
30 views

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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0answers
18 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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0answers
27 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 ...
3
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1answer
64 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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0answers
22 views

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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0answers
28 views

Meaning of the Flags attribute returned by Entrez.esummary(db='nuccore')

My Question Calling Entrez.esummary for the nuccore db returns records with various fields. One of these fields is Flags. I ...
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0answers
21 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 ...
1
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3answers
59 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 ...
1
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1answer
424 views

Downloading SRA Files from AWS

I want to download the original BAM files that the authors had uploaded to SRA. Normally, I would just use sam-dump, but the files are having issues that seem ...
3
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3answers
1k views

How do I pull singe cell RNA sequencing data from GEO database?

I am new to R and computational biology. I am trying to look through a published data set to check for gene expression for my own project. I am having trouble finding materials to teach me how to ...
2
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0answers
182 views

Cannot blast against specific NCBI databases

I am having issues with some prokaryote reference genome databases (exact names : ref_prok_rep_genomes.*), that I downloaded from the NCBI website : https://ftp.ncbi.nlm.nih.gov/blast/db/. Files in ...
1
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1answer
48 views

SRA run data access

Trying to download run data of Run accession SRR2155174. Here's the link: https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR2155174 Please go to the link and go to the "Data Access" tab. Hereunder ...
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1answer
52 views

NCBI SRA database sample: control vs test

I was trying to download some data from NCBI SRA (SRA059451). There are 27 samples available for SRA059451. But i am unable to understand which samples are 'control' and 'test' samples. Please help me ...
2
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1answer
63 views

Translating a genome sequence into possible frames

I have a sequence below from MYC gene about which I need to translate the sequence in all possible frames AND identify (for each frame) which codons are actually used in MYC ...
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2answers
68 views

efetch nucleotide -> protein ids

I'm downloading translated viral genomes initially via Blast - which had shortcomings - and now by efetch. What I want to do is obtain a complete list of all ...
2
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2answers
69 views

How to download multiple proteomes at once?

I'm looking for a way to download multiple proteomes at once from one clade, as fasta. Probably from the NCBI, because it looks more user-friendly than Ensembl, but Ensembl is okay too. In the best ...
2
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1answer
45 views

Why do these NCBI representative genomes for ape species have no Y chromosome?

I recently downloaded a genome from NCBI for chimpanzee and was surprised to see no Y chromosome. I added in one from a separate accession and carried on, but then today went to do the same for ...
5
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1answer
163 views

which NCBI tool is optimized to identify a species from a DNA fragment?

“The Iceman” was a man who lived 5300 years ago and whose body was recovered from an Alpine glacier in 1991. Some fungal material was recovered from his clothing and sequenced. Ice man : found as a ...
0
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1answer
21 views

SRA Toolkit and lebanese data

I am trying to extract data from this: https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR6245218 I installed SRA Toolkit, downloaded the SRR6245218 file and executed this: ...
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2answers
38 views

how to search NCBI to find all available reviewed accession numbers for a protein family

what is the most optimal keyword search query to input into NCBI In order to find all the available proteins accession numbers for a specific family? For example, how would I find all the reviewed ...
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5answers
6k views

How to download FASTA sequences from NCBI using the terminal?

I have following accession numbers of the 10 chromosomes of Theobroma cacao genome. ...
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0answers
37 views

How can extract the list of genes name from the raw data in GEO?

The format of the raw data that upload in GEO is different, like TXT, CEL or other form. How can I extract the list of genes name from these formats? And then how can I normalize them with R? I would ...