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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

205 questions
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Web scraping with Google Script, asynchronous website?

I want to scrape this specific information "NM_000014.5" from the RefSeq transcripts table (to be more specific I'd like to have the RefSeq Select one) of this website https://www.ncbi.nlm.nih.gov/gene/?term=%22A2M%22+human I want to scrape this…
Shinobe
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Use XPATH to obtain value from a large NCBI XML file

I am new to R. I have downloaded the XML with all Bioprojects from the NCBI. The file is 1GB in size. I started with this: setwd("C://Users/USER/Desktop/") xmlfile = xmlParse("bioproject.xml") root = xmlRoot(xmlfile) xmlName(root) [1]…
Guillermo F. Pérez
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Getting protein FASTA sequence based on keyword with python

I would like to gather proteins FASTA sequence from Entrez with python 2.7. I am looking for any proteins that have the keywords: "terminase" and "large" in their name. So far I got this code: from Bio import Entrez Entrez.email =…
tahunami
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Pubmed DataSet - Connecting FTP with Flume

To retrieve the datas from Pubmed DataSet [ncbi], I used FireFTP Addon (in firefox) to retrieve the xml, pdf, txt contents. [http://www.ncbi.nlm.nih.gov/pmc/tools/ftp/] I have successfully installed Apache Flume. The main objective is -- I need to…
Soundarya Thiagarajan
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Best way to crawl a page with multiple redirects

I want to crawl the NCBI website and send request for protein local alignment available at this link: http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch I would like to know if I am able to submit a…
Madrugada
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Extracting a value from a combination of list of dictionaries

The eutils package form NCBI returns the below object for a specific request. From this I want to extract the value 245540. How can I do that? [{u'LinkSetDb' : [{u'DbTo' : 'sra', u'Link' : [{u'Id': '245540'}],…
Vaisakh Viswanath
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Find sequences that does not match to a target sequence

An interesting question by Rnaer from Biostar: I want to find unique dna/protein sequences of a given length (30nt, for example) that does not match to any region of the C.elegans genome. Is there any tool to do that?
hello_there_andy
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Parsing XML object in python 3.9

I'm trying to get some data using the NCBI API. I am using requests to make the connection to the API. What I'm stuck on is how do I convert the XML object that requests returns into something that I can parse? Here's my code for the function so…
user16168208
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How do I print a specific string out of a dictionary element?

SOLVED: Its a a key in a dictionary embedded as an element in a list print(read[0]["Title"]) Heres a picture of the output I am trying to print the article titles (end of line 2) from this esummary request. However, I am unfamiliar with dictionary…
An amateur Programmer
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