Diversas bases de dados e ferramentas


Listas

Biological Databases for Human Research - Um artigo que revê e principalmente classifica os diferentes tipos de bases de dados biológicas https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4411498/

SciCrunch Registry - Portal do NIH de acesso a diferentes bases de dados e ferramentas https://scicrunch.org/browse/resourcedashboard

ALLBIO-TOOLS - Lista bastante exaustiva de bases de dados e ferramentas bioinformáticas http://bioinformatics.hgen.slu.se/ALLBIO-TOOLS/


Portais

EBI (European Bioinformatics Institute) https://www.ebi.ac.uk

GenBank NIH genetic sequence database https://www.ncbi.nlm.nih.gov/genbank/

DDBJ DNA Data Bank of Japan https://www.ddbj.nig.ac.jp/index-e.html

BioCyc collection of 13075 Pathway/Genome Databases (PGDBs), plus software tools for exploring them https://biocyc.org

DAVID (Database for Annotation, Visualization and Integrated Discovery) https://david.ncifcrf.gov

Genomics Portals http://www.eh3.uc.edu/GenomicsPortals/

RefSeq NCBI reference sequences https://www.ncbi.nlm.nih.gov/refseq/

UCSC genome browser (com acesso a diversas ferramentas de análise) https://genome-euro.ucsc.edu/cgi-bin/hgGateway


Text-Mining

PubTator NCBI https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/

ChiliBot Mining PubMed for Relationships http://www.chilibot.net/index.html


Variação

dbGAP NCBI database of Genotypes and Phenotypes https://www.ncbi.nlm.nih.gov/gap

dbSNP NCBI Search small variations in dbSNP or large structural variations in dbVar https://www.ncbi.nlm.nih.gov/projects/SNP/


Expressão genética

GEO (Gene Expression Omnibus) NCBI functional genomics data repository supporting MIAME-compliant data submissions https://www.ncbi.nlm.nih.gov/geo/


Metabolismo

Ingenuity QIAGEN Pathway Analysis tool https://www.qiagenbioinformatics.com/products/ingenuity-pathway-analysis/

BRENDA (Braunschweig Enzyme Database) https://www.brenda-enzymes.org

KEGG (Kyoto Encyclopedia of Genes and Genomes) http://www.genome.jp/kegg/

WikiPathways https://www.wikipathways.org/index.php/

PubChem NCBI chemistry database https://pubchem.ncbi.nlm.nih.gov

OpenPhacts pharmacological data resources https://www.openphacts.org


Interações

BioGRID Biological General Repository for Interaction Datasets https://thebiogrid.org

STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) https://string-db.org

JASPAR transcription factor binding profiles http://jaspar.genereg.net


Proteínas

CDD NCBI Conserved Domains and Protein Classification https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml

ExPASY Swiss Institute of Bioinformatics (SIB) Bioinformatics Resource Portal https://www.expasy.org e também https://www.sib.swiss/services-resources/databases-tools ou por exemplo https://www.expasy.org/proteomics

GPM (The Global Proteome Machine) https://gpmdb.thegpm.org

PeptideAtlas tandem mass spectrometry proteomics experiments http://www.peptideatlas.org

PIR (Protein Information Resource) https://pir.georgetown.edu

RCSB PDB (Protein Data Bank) 3D shapes of proteins, nucleic acids, and complex assemblies http://www.rcsb.org

iHOP (Information Hyperlinked Over Proteins) text mining (inaccessível?) http://www.ihop-net.org/UniPub/iHOP/


Organismos

FlyBase Database of Drosophila http://flybase.org

MGI (Mouse Genome Informatics) Jackson Laboratory http://www.informatics.jax.org

SGD (Saccharomyces Genome Database) https://www.yeastgenome.org