Join GitHub today
GitHub is home to over 28 million developers working together to host and review code, manage projects, and build software together.Sign up
A Meta-database of Low Temperature Genomes and Metagenomes http://reric.org/work/hima/
Fetching latest commit…
Cannot retrieve the latest commit at this time.
|Type||Name||Latest commit message||Commit time|
|Failed to load latest commit information.|
HIMA: A META-DATABASE FOR GENOMES, METAGENOMES, AND PHENOTYPES FROM COLD ENVIRONMENTS R. Eric Collins Ocean Sciences Meeting 2012 The recent flood of sequencing data has been a boon for the traditionally data-poor discipline of biology, but can also prove overwhelming. For microbial ecologists, it would be useful to access a database of phenotypic traits for cultured species of microorganisms, but there does not yet exist a comprehensive database linking genome, taxonomy, and phenotype from environmental isolates; neither are detailed metadata always submitted by sequencing facilities and investigators. For example, no queryable database exists to get a list of all known strains of Bacteria that reduce sulfate, or strains which grow at temperatures below 10˚C. As an initial foray into a web-based database linking phenotype and genotype, I have created a database linking sequences and phenotypic data (which are often archived in disparate locations and formats) of cold-active microorganisms from all three Domains of Life. When available, I include sampling environment, location, temperature and growth range, depth, sequencing platform, amount of data, etc. Currently, the database includes 50 complete genomes sequences as well as 444 metagenomes, including a number of transcriptomes and viromes. Isolates and environmental samples, collected between 79˚N and 77˚S, come from many environments. The database—called 'hima' after the Sanskrit word for snow or cold—will be updated into the future and further expanded to include analytical resources; it can be accessed at http://reric.org/work/hima/.