Access to Sequenced Data and Related Information Flashcards
3 Main Nucleotide Sequence Database
GenBank
European Nucleotide Archive
DNA Database of Japan
National Center for Biotechnology Information (NCBI) of the National Institutes of Health (NIH) in Bethesda
GenBank
European Molecular Biology Laboratory (EMBL)-Bank Nucleotide Sequence Database at the European Bioinformatics Institute (EBI) in Hinxton, England
European Nucleotide Archive
National Institute of Genetics in Mishima
DNA Database of Japan
Other Common Biological Database
PubMed
UCSC
Genome Browser
e!Ensembl
FlyBase
UniProt
WormBase
GENEONTOLOGY
RCSB PROTEIN DATA BANK
tair
Rice Genome Annotation Project
Kyoto Encyclopedia of Genes and Genomes (KEGG)
Types of Biological Data
Genomic Databases
RNA Databases
Protein Databases
Genomic Databases (3)
Sequenced Tag Sites (STS)
Genome Survey Sequences (GSSs)
High-Throughput Genomic Sequence (HTGS)
which genomic database?
= short (typically 500 base pairs long)
genomic landmark sequences
Sequenced Tag Sites (STS)
Which genomic database?
= consist of sequences that are genomic in origin
Genome Survey Sequences (GSSs)
Which genomic database?
= contains unfinished DNA sequences from sequencing centers
High-Throughput Genomic Sequence (HTGS)
Which RNA database?
= contain sequence data on “single-pass” cDNA sequences
Expressed Sequence Tags (ESTs)
Which RNA database?
= (unique gene) created for gene-oriented clusters by making nonredundant sets of ESTs
UniGene
Which protein database?
is the most comprehensive, centralized
protein sequence catalog
UniProt (aka Universal Protein Resource)
RNA Databases (2)
Expressed Sequence Tags (ESTs)
UniGene
Key databases of UniProt:
Swiss-Prot
TrEMBL
PIR
key database under UniProt
= considered the best-annotated protein database (structure and function)
Swiss-Prot
Key database under UniProt
= translated EMBL-NSDL provides automated annotations of proteins
TrEMBL