Chapter 3 - Bioinformatics databases and toolsBioinformatic databasesBioinformaticsBiological researchData analysisEBIENSEMBLEntrezGenome databaseNARNCBIdoi:10.1016/B978-0-323-91128-3.00009-4Mohammad Yaseen SofiAfshana ShafiKhalid Z. MasoodiElsevier Inc.
The European Molecular Biology laboratory (EMBL), the National Center for Biotechnology Information (NCBI), and the DNA Databank of Japan (DDBJ) have been catering to the needs of the researchers around the globe for decades, and the databases and tools hosted by these institutes are continually...
Guest Editorial: Databases and Bioinformatics ToolsNo abstract is available for this article.doi:10.1002/ijch.201310004Prilusky, JaimeSussman, Joel L.John Wiley & Sons, Ltd.Israel Journal of Chemistry
Systems biology requires the integration of data from various sources and their combined interpretation using different bioinformatics tools. Integration of different biological databases, however, is often problematic due to their seman... C Choi,R Münch,B Bunk,... - 《Journal of Integrative Bioinf...
and unsupervised machine learning methods have been employed in binning. Genome binning belonging to unsupervised method clusters contigs into individual genome bins by machine learning methods without the assistance of any reference databases. So far a lot of genome binning tools have emerged. ...
Public databases, such as GreenGenes, often contain many entries for the same species. The common enteric species Escherichia coli, for example, has 44 separate entries in the Greengenes database. Without additional classification such as subspecies or serovars, these entries clutter visual ...
Parallelized molecule and protein sequence retrieval from several online databases, like PubChem, ChEMBL, KEGG, DrugBank, UniProt, RCSB PDB, etc. Loading molecules stored in SMILES/SDF files and loading protein sequences from FASTA/PDB files ...
please refer to 9.3.1.1.10. TCGA for the details about comprehensive data downloading, preprocessing and the features of each data type this present section is focused on the pipeline for downloading and preprocessing of each specific data type ...
Computational methods and resources for CRISPR-Cas investigations, including sgRNA design, repair outcome prediction, editing outcome evaluation, and sgRNA associated repositories and databases, were also discussed (Sledzinski et al., 2020). 3. CRISPR-Cas9 sgRNA design sgRNA design is presumably the ...
32 In addition, allergen sequences from SDAP can be directly searched against protein sequences in the NR and PDB databases at the NCBI using a BLAST search33 implemented in SDAP. Peptide search Allergenic proteins are known to be cross-reactive if they have high sequence or structural ...