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10 votes

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

Entrez Direct is perfect for this sort of thing. You can do something like this: ...
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10 votes
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Importing GFF file with Biopython

No, there is currently no GFF support in biopython. However, you can read in GFF files into python using this package, gffutils. There are also a few other packages to read/write GFF files, like <...
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9 votes
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How to download FASTA sequences from NCBI using the terminal?

Alternatively, you can use the NCBI Entrez Direct UNIX E-utilities Basically, you have to download the install file here: https://www.ncbi.nlm.nih.gov/books/NBK179288/bin/install-edirect.sh In the ...
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  • 1,021
7 votes
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Why do these NCBI representative genomes for ape species have no Y chromosome?

tl;dr: technical difficulties, or sex For the gorilla, that genome is from a female gorilla (Kamilah the gorilla) so she doesn't have a Y chromosome. For the chimp link, there is a visualization of ...
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6 votes

How do you download stuff from NCBI fast?

Answers to this question can be found on biostars. To give you a short summary: Faster way might be to use the parallel-fastq-dump, as suggested in this answer. I ...
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  • 3,521
6 votes

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

Do you mean the NCBI taxonomy IDs? If so, I've personally always preferred the way UniProt displays NCBI taxonomy, and it's easier to download IDs in mass. For example, if you find E.coli's entry: ...
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5 votes

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

The simplest would be using a count matrix (at the end of the link you have shared, section "Supplementary file"). For example ...
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  • 3,472
5 votes

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

I would just blast it. When blasting locally, you need to first make a database from your genome, so assuming you got the command-line version of blast installed you can do something like ...
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  • 5,287
5 votes
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How to get the number of complete phage genomes available on ncbi?

Go to the NCBI nuccore database, at https://www.ncbi.nlm.nih.gov/nuccore Copy and paste the search term: ...
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  • 6,992
4 votes

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

It sounds like your easiest option is to just install blast on your local machine and set up the databases there. It really will only take a few minutes to blast 6,000 sentences against a yeast genome ...
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4 votes

How to download FASTA sequences from NCBI using the terminal?

Just wget or curl each as ...
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  • 3,434
4 votes
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CDS length for each human gene

While I haven't found a way to limit the results to the canonical transcript only, you can get a list of genes, transcripts and their CDS lengths using Ensemble's BioMart. I have already set it up for ...
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  • 7,957
4 votes
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How to retrieve the DNA sequence from a particular species and region through command line?

Samtools Samtools is a toolkit that includes a binary called samtoools, which can be used to query a FASTA file — to extract a subsequence based on some coordinate ...
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4 votes

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

In your sequence header you will see: [location=complement(940023..940580)] It's a reverse strand gene. Reverse complement the sequence, then search the genome ...
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4 votes

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

I think this could be close to what you're looking for: http://glad4u.zhang-lab.org/index.php Paper: GLAD4U: deriving and prioritizing gene lists from PubMed literature It works with gene names though,...
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3 votes
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NCBI retrieve genome assembly with splicing or "modifications"

The page you link to is a GenBank Flat file, the default format used by GenBank. So, to get that format, which includes the join lines, use: ...
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  • 7,957
3 votes
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ncbi...eutils/esearch.fcgi: How to search now in the snp database?

eUtilities for dbSNP is in the process of being retired. See this post from NCBI. You may want to check out the new API. From the NCBI Insights blog post: Entrez search is available only for human. ...
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3 votes

Genomics: Downloading genomic data from the NCBI Genbank database

For downloading data from commandline use the E-utilities of NCBI.
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  • 273
3 votes

Download proteomes from NCBI based only on binomial names

The general procedure is explained here: First step is to search the Taxonomy database with the organism name. Accepted common names usually work at all taxonomic levels. Use the scientific name or ...
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  • 451
3 votes
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How to automate NCBI genome download

Outline of solution: get this file: ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt filter for lines having "Complete Genome" in column 12 filter for lines having a taxid (...
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3 votes

NCBI xml-format Printing nodeValues from tags with the same names

use a XSLT processor (http://php.net/manual/en/class.xsltprocessor.php) with the following stylesheet. ...
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  • 1,473
3 votes

NCBI SRA database sample: control vs test

You can download the information using this link: I did it in R: ...
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  • 1,638
3 votes

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

I haven't done any whole-genome STR analysis from NGS data myself, but are aware of others that have used lobSTR for this. There's also a recent paper [here] that compares a few different STR analysis ...
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  • 11.5k
3 votes

How to extract metadata from NCBI's experiment?

You'll want something like: esearch -db sra -query SRX1596422 | efetch -format runinfo This will produce a CSV output to the screen with columns containing the ...
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3 votes
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Programmatically retrieve Metadata from SRA Run Selector

Depending on exactly which information you seek, you can try: esearch -db sra -query 'PRJNA491191[bioproject]' | efetch -format native -mode xml This will return ...
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3 votes
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What does this accession NCBI code mean: 6MWN_B?

In general, an accession is a value that points to (provides access to) a single database entry. Different databases (GenBank, RefSeq, Ensembl, SwissProt, and so on) have different conventions for ...
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2 votes

How to automate NCBI genome download

As an alternative, you can use the NCBI Datasets CLI, in a two step process to generate a dehydrated dataset for later hydration: ...
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2 votes

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

You can use Entrez Direct for this as follows: efetch -db protein -id YP_805528.1 -format gpc -mode xml | xtract -insd Protein EC_number YP_805528.1 6.3.2.13
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  • 1,126
2 votes

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

Here's a very crude script version, which should work without downloading fancy software tools. It will only work as long as the website stays in its current layout. It extracts the particular ...
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  • 309
2 votes

Importing GFF file with Biopython

I would use BCBio for gff handling as it is written to directly interface with BioPython’s object model. The only downside is that I believe it is no longer ...
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