LSM2241 Practical 2

Part 0
Exploring Bioinformatics Databases and
Tools
Review of Practical 1
Explored PubMed and Google Scholar
Traced articles upstream and downstream
by citations
Reference management
TP/FP/TN/FN
Objectives for Practical 2
Use multiple approaches to find different types of biological data through
the NCBI Entrez system
Formulate queries of selected databases
Wild-card
Boolean
Field-specific
Assess quality of searches
Specificity
TP/FP/TN/FN
Distinguish information contained in NCBI Gene, Protein, and nucleotide
sequence databases
Critically distinguish RefSeq entries on the basis of prefixes and status
codes
Objectives for Practical 2 contd
Take note of database identifiers and use them to interrogate unlinked
databases
Use database cross-references to link to other databases
Relationship between orthologs and paralogs, and the derivation of RefSeq
Entries
Evolutionary relationships encoded in PAM matrices
Introduction to Biological Databases
NCBI: Molecular biology resource that provides useful bioinformatics
analysis tools as well as biological databases
PubMed: Literature
RefSeq: Reference (representative) sequences
Gene: Locus-centered gene information
Protein: Protein sequences
OMIM: Online Mendelian Inheritance in Man- genetic disorders
UniProt: Protein sequences and functional information
Enzyme: Enzyme information
KEGG Pathways: Bio-molecular pathways diagrams
PDB, MMDB: 3D biological structures
Why Bother?
But
Literature search?
There are so many databases!