snhs-BSBio.jpg (39763 bytes)

BIO 300 (M5) / MAT 300 (01): Bioinformatics

bu-spin-shield.gif (17879 bytes)      dna1.gif (13700 bytes)

 

BLAST EXERCISE

NCBI logo NCBI banner
PubMed All Databases BLAST OMIM Books TaxBrowser Structure

 

Nucleotide

bullet

Quickly search for highly similar sequences (megablast)

bullet

Quickly search for divergent sequences (discontiguous megablast)

bullet

Nucleotide-nucleotide BLAST (blastn)

bullet

Search for short, nearly exact matches

bullet

Search trace archives with megablast or discontiguous megablast

Protein

bullet

Protein-protein BLAST (blastp)

bullet

Position-specific iterated and pattern-hit initiated BLAST (PSI- and PHI-BLAST)

bullet

Search for short, nearly exact matches

bullet

Search the conserved domain database (rpsblast)

bullet

Protein homology by domain architecture (cdart)

 

{1} Do a BLAST search on the following nucleotide sequences:

a)  NSeq1: [5' GAACTTGTTATTTCT 3']

b)  NSeq2: [5' GAGTTAGTGATAAGT 3']

c)  NSeq3:  [5' CCAGAAACAGAGAGATTAATAAAC 3']

 

bullet

BLAST :  Search for short, nearly exact Nucleotide Sequence matches [Right click, Open in new window]

 

 

{2} Translate the following nucleotide sequence:

a)  NSeq1: [5' GAACTTGTTATTTCT 3']

b)  NSeq2: [5' GAGTTAGTGATAAGT 3']

c)  NSeq3:  [5' CCAGAAACAGAGAGATTAATAAAC 3']

 

 

bullet

Complementary & Sequence Translation (SEMO)

 

 

{3} Do a BLAST search on the above Translated Protein Sequences:

a)     PSeq1:  Protein sequences [1.1-1.6] ___________________

b)     PSeq2:  Protein sequences [2.1-2.6] ___________________

c)     PSeq3:  Protein sequences [3.1-3.6] ___________________

 

 

bullet

Search for short, nearly exact Protein Sequence matches [Right click, Open in new window]

 

 

{4} Result & Conclusion:

Result & Conclusion Clck on Picture on the left to check for Result

 

 

 

 

 

{5} What do you think the following sequence will be translated into ???

NSeq3: "CCGCGGGAGTCGTTGGAGTAC"

Answer: Presley

 

 

Answer: Elvis Elvis candidatus

Answer: Elvis Key1a

 

 

Back to "Bioinformatics HomePages"