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w.ebi.ac.uk/biocat/Oligomer_design_and_synthesis.html">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 with the '-ONEintothree' option, and your input sequence file can be either GCG format or any of the other formats that Reformat accepts. Note that reformat will write over your input sequence file, so save a copy if you want to preserve the original!

Sample session:
helix% more jc5122.pir2 P1;JC5122 - superoxide dismutase (EC 1.15.1.1) (Mn) precursor - Caenorhabditis elegans C;Species: Caenorhabditis elegans C;Date: 02-Feb-1997 #sequence_revision 27-Feb-1997 #text_change 13-Mar-1997 C;Accession: JC5122; JS0750 [...etc etc....] jc5122.pir2 Length: 221 August 14, 1997 10:53 Type: P Check: 1490 .. 1 MLQNTVRCVS KLVQPITGVA AVRSKHSLPD LPYDYADLEP VISHEIMQLH 51 HQKHHATYVN NLNQIEEKLH EAVSKGNVKE AIALQPALKF NGGGHINHSI 101 FWTNLAKDGG EPSAELLTAI KSDFGSLDNL QKQLSASTVA VQGSGWGWLG 151 YCPKGKILKV ATCANQDPLE ATTGLVPLFG IDVWEHAYYL QYKNVRPDYV 201 NAIWKIANWK NVSERFAKAQ Q helix% reformat -oneintothree Reformat rewrites sequence file(s), scoring matrix file(s), or enzyme data file(s) so that they can be read by GCG programs. REFORMAT what sequence file(s) ? jc5122.pir2 jc5122.pir2 length: 663 aa helix% more jc5122.pir2 P1;JC5122 - superoxide dismutase (EC 1.15.1.1) (Mn) precursor - Caenorhabditis elegans C;Species: Caenorhabditis elegans C;Date: 02-Feb-1997 #sequence_revision 27-Feb-1997 #text_change 13-Mar-1997 C;Accession: JC5122; JS0750 [... etc etc ...] F;50,98,182,186/Binding site: manganese (His, His, Asp, His) #status predicted jc5122.pir2 Leng