Bioinformatics and the Internet: Tools of the Trade

Or...how to use online tools to do useful stuff with biological data.

Objective

Learn how to use sequence data to characterize and compare genes and proteins. “What protein does my DNA sequence encode for, and what does it do?”

Activity

Find a functional gene in a sample of unknown sequence, determine what protein it encodes, find a similar gene/protein in humans.

Translation and ORF location with Expasy

Expasy: http://web.expasy.org/translate/

Gene-protein identification with BLAST

BLAST: http://blast.ncbi.nlm.nih.gov/

Protein structure and function

PDB: http://www.rcsb.org/

PFAM: http://pfam.xfam.org/family/PF00225

CATH: http://www.cathdb.info/

File
unknown_genomic_sequence.fasta_.txt