Research tasks for this unit (due March 25, 2023)
Important Instructions:
• Your narrative has to reflect your understanding of the databases and browses that
you describe.
• For each database, in addition to your description of the database, you must
provide the most current database statistics reported by the database itself (such
as the most current number of sequences, base pairs etc.).
• Make sure that you follow all report and submission requirements as specified
in Syllabus (including the rules on quotations, citations, and plagiarism).
Task 1: Protein sequence or structure databases:
a) Select one of the following databases and provide its detailed description:
• UniProt
• RefSeq
• Protein Data Bank (PDB) (Choose this one for this question)
b) Provide a concise but informative description of one of the remaining databases.
Task 2: Browsers / Portals:
a) Select one of the following systems and provide its detailed description:
• UCSC Genome Browser
• Ensembl Genome Browser (Choose this one for this question)
• NCBI Genome Data Viewer (GDV Browser)
• ExPASy Bioinformatics Resources Portal
b) Provide a concise but informative description of one of the remaining systems
Citiations to use:
Nucleic Acids Research, 2023, Vol. 51, Database issue
https://academic.oup.com/nar/issue/51/D1#1568846-6880745
NCBI database resources
https://academic.oup.com/nar/article/51/D1/D29/6825348
GenBank 2023 Update
https://academic.oup.com/nar/article/51/D1/D141/6814443
GenBank website
http://www.ncbi.nlm.nih.gov/genbank/
European Nucleotide Archive
https://academic.oup.com/nar/article/51/D1/D121/6833239
ENA website
http://www.ebi.ac.uk/ena
DNA Data Bank of Japan
https://academic.oup.com/nar/article/51/D1/D101/6845431
DDBJ website
http://www.ddbj.nig.ac.jpStarting points:
Nucleic Acids Research, 2023, Vol. 51, Database issue
https://academic.oup.com/nar/issue/51/D1#1568846-6880745
NCBI database resources
https://academic.oup.com/nar/article/51/D1/D29/6825348
GenBank 2023 Update
https://academic.oup.com/nar/article/51/D1/D141/6814443
GenBank website
http://www.ncbi.nlm.nih.gov/genbank/
European Nucleotide Archive
https://academic.oup.com/nar/article/51/D1/D121/6833239
ENA website
http://www.ebi.ac.uk/ena
DNA Data Bank of Japan
https://academic.oup.com/nar/article/51/D1/D101/6845431
DDBJ website
http://www.ddbj.nig.ac.jpStarting points:
UniProt
https://academic.oup.com/nar/article/51/D1/D523/6835362
UniProt website
http://www.uniprot.org/
RefSeq website
http://www.ncbi.nlm.nih.gov/refseq/
Protein Data Bank
https://academic.oup.com/nar/article/51/D1/D488/6845439
PDB website
http://www.wwPDB.org
UCSC Genome Browser
https://academic.oup.com/nar/article/51/D1/D1188/6845436
UCSC Genome Browser website
http://genome.ucsc.edu
Ensembl
https://academic.oup.com/nar/article/51/D1/D933/6786199
Ensembl website
http://www.ensembl.org
ExPASy website
http://www.expasy.org
NCBI Genome Data Viewer
https://www.ncbi.nlm.nih.gov/genome/gdv/