Questions tagged [ncbi]

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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
1 vote
2 answers
149 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 ...
2 votes
1 answer
104 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 + <...
0 votes
1 answer
102 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 vote
1 answer
60 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, ...
2 votes
2 answers
2k 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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1 vote
0 answers
27 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
37 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 ...
  • 101
1 vote
0 answers
21 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 ...
3 votes
1 answer
100 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
60 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 ...
1 vote
0 answers
45 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 vote
3 answers
301 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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3 votes
1 answer
1k 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 ...
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3 votes
3 answers
3k 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 votes
0 answers
492 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 vote
1 answer
64 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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1 vote
1 answer
65 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 ...
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2 votes
1 answer
69 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 ...
0 votes
2 answers
97 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 ...
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2 votes
2 answers
211 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 ...
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3 votes
1 answer
60 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 ...
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5 votes
1 answer
252 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 votes
1 answer
24 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: ...
0 votes
2 answers
48 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 ...
10 votes
5 answers
15k views

How to download FASTA sequences from NCBI using the terminal?

I have following accession numbers of the 10 chromosomes of Theobroma cacao genome. ...
1 vote
1 answer
70 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 ...
2 votes
3 answers
2k views

CDS length for each human gene

Does anyone know where and how could I download a list of all human genes and the length of the coding sequence for each gene? Is it possible to do this on the NCBI site, ensembl?
1 vote
1 answer
46 views

NCBI retrieve genome assembly with splicing or "modifications"

I am trying to fetch genome assemblies that include splicing information. E.g. Here, is a genome assembly of a yeast, where genes show variants like this: ...
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3 votes
2 answers
642 views

How do you download stuff from NCBI fast? [duplicate]

I have 2 .csv files that contains a list of accession codes. For example for this experiment a .csv file will contain: ...
  • 1,417
2 votes
1 answer
98 views

What is the recognized way to reference accession data (.sra files) from NCBI as a URI?

I would like to assign a URL/URI to accession runs (i.e. SRR IDs) from the NCBI short read archive. In program listings, I used to list them as ftp:// URLs, ...
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5 votes
6 answers
2k views

How to extract metadata from NCBI's short read archive (SRA) for a few runs?

I wish to extract metadata from a list of runs on NCBI's short read archive. For instance, I'd like to extract the library name ("HS0798") from the following run info: https://trace.ncbi.nlm.nih.gov/...
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3 votes
2 answers
168 views

wget for links inside html pages

I am trying to download a file from the following repository: https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR7276474 As you can see, there are several layers to the webpage. For example, clicking ...
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4 votes
1 answer
51 views

How to export web NCBI tBLASTn results in table format with many queries?

Context I'm an MSc student working on writing up my thesis (back home now) from my laptop and, therefore, unfortunately don't have access to a workstation/server capable of doing the tBLASTn search ...
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1 vote
1 answer
102 views

Are there free cloud computing platforms for biology projects? [duplicate]

I want to implement the analysis found in the paper RNA-Seq of Tumor-Educated Platelets Enables Blood-Based Pan-Cancer, Multiclass, and Molecular Pathway Cancer Diagnostics The project id is 281708. ...
7 votes
3 answers
1k views

Importing GFF file with Biopython

Is there a way to import a GFF file for an organism with Biopython in the same way you can for a Genbank file? For example, ...
1 vote
1 answer
124 views

ncbi...eutils/esearch.fcgi: How to search now in the snp database?

According to the 2017(!) textbook, it worked at that time, for instance, https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=snp&term=autism At ...
1 vote
1 answer
488 views

Python scripting with ete3 to query NCBI's Taxonomy: "sqlite3 Warning (can only execute one statement at a time)"

I am using this script: ...
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7 votes
1 answer
344 views

ANY (technical) reason behind submitting sequences to GenBank versus ENA Sequence

The DNA sequence sections of the three INSDC databases (i.e., DDBJ, ENA Sequence and GenBank) are synchronized periodically and strive to keep their stored data as ubiquitously accessible as possible. ...
1 vote
1 answer
87 views

Genomics: Downloading genomic data from the NCBI Genbank database

I'm taking a genomics course at school, and we have a final project due in a few weeks. Now, I can write bash scripts to sort and analyze the data, etc. However, I'm not quite sure how to actually ...
user avatar
1 vote
1 answer
304 views

Mapping RefSeq-ID or NCBI-ID (Entrez-ID) to EC number

I annotated my bacterial genomes using the new NCBI Prokaryotic Genome Annotation Pipeline and now, I want to annotate EC-numbers. In the master annotation file (.gff), I get the RefSeq-ID of every ...
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2 votes
0 answers
39 views

Does anyone have older versions of NT and 16s RNA DB from NCBI?

I am in search of past years' versions of NT and 16s databases from NCBI. I recently contacted NCBI about this and they replied: Unfortunately, we do not archive past versions of the blast ...
  • 245
7 votes
1 answer
82 views

Source for whole genome comparisons at NCBI Genomes

The NCBI Genomes database has these dendrograms for (presumably) whole genome comparisons for certain species, e.g. Pseudonomas aeruginosa or Escherichia coli. How were these comparisons done? ...
4 votes
2 answers
1k views

How to automate NCBI genome download

I need to download all the completely assembled cyanobacterial genome's GenBank file(.gbff) from NCBI(RefSeq or INSDC ftp data). For this I think, the steps are: Need to find the completely ...
0 votes
1 answer
28 views

Genebank Submission

I am not sure this kind of question is allowed here. I am asking because some of you might have already experienced this. I submitted some virus genomes in the Genebank. The genomes are on hold and ...
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2 votes
2 answers
1k views

Retrieving NCBI Taxa IDs from refseq or GenBank assembly accession

I have about 10,000 genome files all named by either refseq or genbank accession number, do you know if it's possible to convert these numbers to the corresponding NCBI taxon ID or species? for ...
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3 votes
2 answers
168 views

Download proteomes from NCBI based only on binomial names

I'm trying to download around 2000 proteomes from NCBI, but all I have is the genus and species e.g: lophodermium_seditiosum trichoderma_harzianum Does anyone know ...
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1 vote
1 answer
2k views

How to interpret a PSSM matrix from PSI-Blast - what do the numbers represent?

PSI-Blast on a sequence returns a PSSM matrix file containing two matrices, one to the left, one the the right, for all amino acids: ...
  • 507
4 votes
1 answer
109 views

What does an output of -I for all amino acids mean in a psi-blast pssm matrix file?

I have run psi-blast using the NR database, remotely, with one iteration, for several sequences to calculate an evolutionary profile (PSSM) for each of those sequences. However, many of the PSSM ...
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