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Databases for Biologists
With the myriad information in today’s digital world, it can be difficult to know where to look for what you really need. Databases are “Google” for scientists, holding thousands of data for endless uses. Here, we have consolidated different scientific databases and repositories to simplify your search, so you can spend more time pioneering science.
Gene Databases
GenBank (NCBI) – a fully annotated, public database of DNA sequences. GenBank is part of an international network of genetic databases that updates and exchanges their data daily.
Ensembl – a genomic database that provides researchers with access to annotated genomes mostly of vertebrate species. Annotations are available at the genome, gene, and protein levels. Additionally, the genome browser provides further information like the effects of sequence variation on protein.
Gene Expression Omnibus (NCBI) – a public repository for genomics data. The repository supports array and sequence-based data. It also provides tools for users to download experiments as well as make gene expression profiles.
Online Mendelian Inheritance in Man (OMIM) – a comprehensive database of myriad human genes and genetic phenotypes. The database is constantly updated and includes information on all mendelian disorders as well as information on 15,000+ genes and counting.
Enzyme Database
BRENDA – a comprehensive database of enzymes and their functions. The information provided in the database is extracted directly from primary literature and is constantly updated.
SNP Database
dpSNP – a database that grants users access to information on the genetic variance within and across different species. The database includes a multitude of different variations including SNPs, short deletion and insertion polymorphisms, short tandem repeats (STRs), multinucleotide polymorphisms (MNPs), etc.
Protein Databases
Protein Data Bank (PDB) – provides information about proteins, nucleic acids, and other biological structures geared to students and researchers in biomedicine and agriculture. The database includes 3-D structures typically obtained usual X-ray crystallography or NMR spectroscopy.
UniProt – a catalog of information on everything related to proteins. The data is collected from a variety of sources like genome sequencing projects and research literature.
Plasmid Repositories
Sigma-Aldrich SnapFast™ – a vector collection developed by Oxford Genetics based on a desire to standardize the cloning process. Vector components can be easily swapped with restriction enzymes in order to easily control the process. The Snapfast™ technology provides users with a plasmid system for creating multiple gene expression systems.
Addgene – a plasmid repository that allows scientists to share plasmids across the research community. Addgene works with labs and researchers to provide high quality, up-to-date information. Their plasmids are also linked to related articles so scientists can receive the correct context when researching and working with these plasmids.
iGEM
iGEM repository – a registry with over 20,000 parts organized by type, function, number of uses etc. iGEM students, graduate students, postdocs, and PIs have all contributed parts to the collection over a period of ten years. This tool is a great way to guarantee success, as users can choose to use parts that have been successfully used countless times before.
It's highly recommended for you to read the article about the many tools and resources available to aid you in your biological research. Here, these databases and repositories round out the list. Addgene and Sigma-Aldrich plasmid repositories, the iGEM repository as well as the NCBI database can all be found integrated within the Genome Compiler platform. This incorporation aligns with Genome Compiler’s “all-in-one” vision. Looking to the future, we hope to integrate more databases and repositories for users to access through the software. We are constantly interacting with users in hope of learning more about your product needs. Discussion is encouraged, so please comment below with feedback on these resources as well as any others you use and would like integrated in the Genome Compiler platform. Enjoy!
Gene Databases
GenBank (NCBI) – a fully annotated, public database of DNA sequences. GenBank is part of an international network of genetic databases that updates and exchanges their data daily.
Ensembl – a genomic database that provides researchers with access to annotated genomes mostly of vertebrate species. Annotations are available at the genome, gene, and protein levels. Additionally, the genome browser provides further information like the effects of sequence variation on protein.
Gene Expression Omnibus (NCBI) – a public repository for genomics data. The repository supports array and sequence-based data. It also provides tools for users to download experiments as well as make gene expression profiles.
Online Mendelian Inheritance in Man (OMIM) – a comprehensive database of myriad human genes and genetic phenotypes. The database is constantly updated and includes information on all mendelian disorders as well as information on 15,000+ genes and counting.
Enzyme Database
BRENDA – a comprehensive database of enzymes and their functions. The information provided in the database is extracted directly from primary literature and is constantly updated.
SNP Database
dpSNP – a database that grants users access to information on the genetic variance within and across different species. The database includes a multitude of different variations including SNPs, short deletion and insertion polymorphisms, short tandem repeats (STRs), multinucleotide polymorphisms (MNPs), etc.
Protein Databases
Protein Data Bank (PDB) – provides information about proteins, nucleic acids, and other biological structures geared to students and researchers in biomedicine and agriculture. The database includes 3-D structures typically obtained usual X-ray crystallography or NMR spectroscopy.
UniProt – a catalog of information on everything related to proteins. The data is collected from a variety of sources like genome sequencing projects and research literature.
Plasmid Repositories
Sigma-Aldrich SnapFast™ – a vector collection developed by Oxford Genetics based on a desire to standardize the cloning process. Vector components can be easily swapped with restriction enzymes in order to easily control the process. The Snapfast™ technology provides users with a plasmid system for creating multiple gene expression systems.
Addgene – a plasmid repository that allows scientists to share plasmids across the research community. Addgene works with labs and researchers to provide high quality, up-to-date information. Their plasmids are also linked to related articles so scientists can receive the correct context when researching and working with these plasmids.
iGEM
iGEM repository – a registry with over 20,000 parts organized by type, function, number of uses etc. iGEM students, graduate students, postdocs, and PIs have all contributed parts to the collection over a period of ten years. This tool is a great way to guarantee success, as users can choose to use parts that have been successfully used countless times before.
It's highly recommended for you to read the article about the many tools and resources available to aid you in your biological research. Here, these databases and repositories round out the list. Addgene and Sigma-Aldrich plasmid repositories, the iGEM repository as well as the NCBI database can all be found integrated within the Genome Compiler platform. This incorporation aligns with Genome Compiler’s “all-in-one” vision. Looking to the future, we hope to integrate more databases and repositories for users to access through the software. We are constantly interacting with users in hope of learning more about your product needs. Discussion is encouraged, so please comment below with feedback on these resources as well as any others you use and would like integrated in the Genome Compiler platform. Enjoy!