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Sciences Library News

Tag: genomes

Image of double helical DNA strands
Aug 10 2018

Natural Language Searching in NCBI Databases

Posted on August 10, 2018 by Laurie Neuerburg

NCBI has improved its search functionality in the “all databases” search to be compatible with natural language searching. In the past, natural language searching for sequence data brought up too many results or sometimes zero results. Now you can search NCBI more intuitively than before and receive good results for genes, nucleotides, and assemblies! How do you get started with NCBI’s new natural language searching?

Go to the homepage of NCBI. The default search shows “All Databases” in the drop-down box. Here you can try out some of the improved search queries:

Genes

  • [Species name] + [gene symbol]
    • Chelonia mydas SDHA

Search result for Chelonia mydas SDHA

  • Rat B2M

Search result for rat B2M

 

Nucleotide Sequences

  • [Species name] + [gene symbol] + mRNA/transcript/CDS
    • Salmo salar SUMO1 mRNA

Search result for Salmo salar SUMO1 mRNA

  • Mus musculus Abcg2 transcript

Search result for Mus musculus Abcg2 transcript

  • Cow CA2 CDS

Search result for CA2 cow CDS

 

Genome Assemblies

  • [Assembly name]
    • GRCz11

Search result for GRCz11

  • [species name] + assembly/genome
    • Chicken assembly

Search result for chicken assembly

  • Escherichia coli genome

Search result for Escherichia coli genome

 

Posted in Biology, DatabasesTagged genes, genomes, natural language searching, NCBI
Image of BioCyc logo
Jun 08 2018

BioCyc: A Collection of Pathway/Genome Databases

Posted on June 8, 2018June 8, 2018 by Laurie Neuerburg

We now have access to BioCyc, a collection of Pathway/Genome Databases (PGDBs). You can search BioCyc by gene, protein, enzyme, or metabolic pathway. You can use advanced tools to view metabolic diagrams, to perform data analysis, and to compare organisms. You can register for a free BioCyc account if you would like to customize your viewing preferences, to create SmartTables to store datasets, and to run and save metabolic models. You can export high-quality metabolic diagrams and create your own PGDB from an annotated genome file. 

 

These organism-specific databases are divided into three tiers based upon the level of data curation, with tier 1 databases having the highest level of curation by scientists. Tier 2 databases have had moderate curation, and tier 3 databases are computationally created with no curation. Examples of the most popular tier 1 databases are Escherichia coli K-12 substr. MG1655 (EcoCyc), Homo sapiens, and Saccharomyces cerevisiae S288c. When you start out in BioCyc, the default organism database is E. coli K-12. To change to a different database, you can click on “change organism database” at the top right of the page. After you choose a new database, you are taken to a summary page for the database. Then you can click on a chromosome (or genome) to view annotations in the genome browser. 

Image of how to change organism database

 

HawkID authentication is required for off-campus use of BioCyc. Do you still have questions? Contact the Sciences Library for help!  

Posted in Biology, DatabasesTagged genetics, genomes, metabolic pathways

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