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e using the begin, end and range information from the framesearch output, and use that as input into Pileup. However, framesearch is much slower than Fasta.

How do I design a primer?

There are several design criteria:

melting temperatures of primer and product
GC content
ambiguous bases
self-complementarity -- how to avoid primer dimer formation and primer secondary structure
size of primer
PCR product length
repeats, e.g. similarity to common rodent repeat sequences

GCG's prime program selects primers, and is also accessible through

GCG-Lite's web interface to prime.

Other web-accessible primer design programs are

Primer3 from the Whitehead Institute,

xprimer from U. Minnesota,

GeneFisher from U. Bielefeld.

Programs than run on Macs and PC's are MacVector for the Mac, GeneWorks for the Mac, OSP for Mac/PC/VAX/Sun/Xwindows, and primegen. Also check EBI's list of primer design programs.

More information about primer design can be found at:

Restriction Maps and PCR primer design, a course at NYU.

PCR primer analysis, a course from U. Kentucky.

How do I convert peptide sequences from 1-letter to 3-letter amino acid codes?

Reformat, which converts other sequence formats into GCG format, can do this. You would run it wi