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Questions tagged [ncbi]

NCBI is a National Center for Biotechnology Information, one of the most important websites used by bioinformaticians. NCBI runs a big variety of various bioinformatical web services, also provides important databases for download.

The NCBI covers a wide range of bioinformatics resources, from journal listing to gene alignments to chemical libraries databases to protein folding prediction.

NCBI's data is publicly available from the main website and from ftp repositories.

  • PubMed
    PubMed, a database of citations and abstracts for biomedical literature from MEDLINE and additional life science journals.

  • The NCBI C++ Toolkit provides a set of modules to access, modify, generate and deposit biological data. The full description can be read in its online book

  • PubChem, a chemical library database, has its own API to search and retrieve chemical compounds

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How to set QNetworkReply properties to get correct NCBI pages?

I try to get this following url using the downloadURL function as follows: http://www.ncbi.nlm.nih.gov/nuccore/27884304 But the data is not as what we can see through the browser, now I know it's because some correct information (such as browser…
Claire Huang
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Using Biopython to retrieve details on an unknown sequence by BLAST

I'm using Biopython for the first time. I have sequence data from unknown organisms, and trying to use BLAST to tell which organism they are most likely to have come from. I wrote the following function to do that: def find_organism(file): """ …
soungalo
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Using Biopython to run a BLAT search through NCBI

I'd like to run several BLAT queries with different sequences and then perform a multiple sequence alignment on the results. How can I use Python to run these BLAT queries? I know that there is a way to use BLAST, but I am not sure about BLAT.
cs4
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PHP Cannot retrieve value from a specific DOM element

I am trying to retrieve content from a p element in this page. As you can see, in the source code there is a paragraph with the content i want:

Actually i want to take the value…
F.N
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Reading a webpage with perl's LWP - output differs from a downloaded html page

I try to access and use different pages in NCBI such as http://www.ncbi.nlm.nih.gov/nuccore/NM_000036 However, when I used perl's LWP::Simple 'get' function, I do not get the same output I get when I save the page manually (with the firefox browser…
user2182857
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Use BLAST SRA function with R

I'm an R noob, but can I control the SRA function in NCBI BLAST from command line in R? The NCBI website is notoriously unreliable, and I'd like to be able to manage batches of files.
user3246796
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Access abstract from pubmed using Bio::DB::EUtilities

I am using Bio::DB::EUtilities to query the Pubmed DB with given PMIDs (Pubmed Id). use Bio::DB::EUtilities; use strict; use warnings; my @ids = (23298400); my $factory = Bio::DB::EUtilities->new(-eutil => 'efetch', …
Matthias Munz
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Local BLAST Swissprot Database error

I am trying to run the standalone ncbi-blast-2.2.28+ on my machine (Mac) but get this error message when running blastp with SwissProt database: BLAST Database error: Could not find volume or alias file (nr.00) referenced in alias file…
lqdo2000
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ORF and amino identification using BioPython's translate() method-- incorrect translations?

I am trying to teach myself bioinformatics, arriving to the party by way of computer science and high performance computing. (Essentially, I'm trying to learn the biology.) I've recently discovered BioPython and so far think it's great, but I am…
HodorTheCoder
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pull xml rss feed from ncbi

so i have this search http://www.ncbi.nlm.nih.gov/pubmed/?term=Streptococcus+dysgalactiae+subspecies+equisimilis and i want to get the rss feed(not manually), like a string with the xml, but i want to do it using php. ive tryed to search for a…
jose bode
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blast given GI NCBI nucleotide database

I have local database driven website which contains a few sequences which are uniquely identified via their GI number. Is it possible to link to the 'NCBI blast site' directly given the GI. For example the sequence for GI 903049 has this…
cs0815
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How can you add to a hash value instead of having it overwrite with the new value?

Basically I have these files (medline from NCBI). Each is associated with a journal title. Each has 0, 1 or more genbank identification numbers (GBIDs). I can associate the number of GBIDs per file with each journal name. My problem is that I may…
kbearski
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How can I choose the longest of each locus?

I have a CSV file that I got from NCBI and I want to select in R the one with the largest value in the "length" column of each repetitive "locus". For example it repeats AGER in the Locus column and when I checked it I need to get it as the longest…
pentro gen
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Extracting a specified data in python from multi url link using bs4

Need help in extracting the data from the Main URL that redirects to the sub URL link in which the required data needs to grep. Main Url = "https://www.ncbi.nlm.nih.gov/gene/{gene_id}" sub Url =…
naoki
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Gene Protein Sequence Database

I am wondering if there is a way to download or retrieve all the protein sequences of Genes from NCBI. I have the lots of GeneIDs I would like to iterate and retrieve their protein sequence. Is there a package I use for this or link to the protein…
Ibk
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