Real Alignments

Table of Contents

Real Alignments

Phylogeny

Cow-to-Pig

Cow-to-Pig cDNA

DNA similarity reflects polypeptide similarity

Coding vs Non-coding Regions

Third Base of Codon Hypervariable

Cow-to-Fish Protein

Cow-to-Fish DNA

Protein vs DNAAlignments

How do I find similar sequences?

Database Alignment

FASTA

Basic BLAST Family

DNA Databases

Protein Databases

BLAST Input

BLAST Strategy

BLASTN Usage/Output

BLASTP Usage/Output

BLASTN

Alignment Statistics

PPT Slide

“Real” Alignments

BLAST Options

Extended BLAST Family

BLAST-next??

Email: staben@pop.uky.edu

Home Page: www.uky.edu/Classes/BIO520/BIO520WWW/

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