Lecture 3.

2a
BLAST
BLAST: Overview
• a tool / algorithm for searching or comparing primary biological
sequence information (amino acids, nucleotides, etc)

•“Google” for DNA/RNA/protein sequences where your input is a

sequence

• match a certain sequence (query) to a database of sequences (subject)

• Web BLAST: https://blast.ncbi.nlm.nih.gov/Blast.cgi

• Local BLAST: downloadable
BLAST: Overview
• Web BLAST: https://blast.ncbi.nlm.nih.gov/Blast.cgi

• Local BLAST: downloadable

Workshop 3.1a
BLAST
BLAST: Workshop
• Google BLAST
• Click the first entry on the results
• Choose Nucleotide BLAST
Paste your consensus sequence here
(Psv corrected)
 Choose Database : others (nr etc.)

Choose Optimize for: Somewhat

similar sequence (blastn)
Click BLAST
Alignment Alignment Score
Coverage (color)
(length)
Lecture 3.2b
GenBank
GenBank: Overview
• an open access database of, publicly available nucleotide
sequences and their protein translations

• produced and maintained by the National Center for

Biotechnology Information (NCBI)

• contains over 150 billion nucleotide bases in more than

162 million sequences as of 2013

• used as a resource for sequence publication and

sequence comparison

•“Google” for DNA/RNA/protein sequences where your

input is a set of words
GanBank: Workshop
• Google GenBank
• Click the first entry on the results
• Choose Nucleotide BLAST
•Ensure that Nucleotide is selected
•Type PEDV Spike
•Click Search
• This can be copied to notepad for
saving to your computer