genomes – Sciences Library News

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

Rat B2M

Nucleotide Sequences

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

Mus musculus Abcg2 transcript

Cow CA2 CDS

Genome Assemblies

[Assembly name]
- GRCz11

[species name] + assembly/genome
- Chicken assembly

Escherichia coli genome

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.