PepMap Explanation

Peptides should be pasted or uploaded in the following format.

	peptide_name (space or tab) peptide
   e.g.   pep1  IRLRPGGKKK 
	  pep2	VSQNYPIVQN

The tool may have difficulty finding the correct location of sequences <8 amino acids.

When this option is checked, peptide maps in HTML and PDF formats will be generated. If this option is unchecked, the tool will work faster, but only the Fasta alignment will be generated.

Mapping results are displayed in several formats.

• Html map links show the location of your queries in the different proteins.
Example:
• Data for download
• All maps in PDF file.
• Peptides mapped to the reference sequence in Fasta format.

• Location Table in simple text format.
• Above data in an archived zip file.
• Location Table in HTML format: provides peptide name, query peptide sequence, matched reference sequence, AA positions in protein and polyprotein. (If the peptide runs through two proteins, for example, starts on p17 and ends on p24, only polyprotein location is shown. Gag in this example).



Epitope Name	Query Peptide	Reference Peptide	Protein	AA position In Protein	Polyprotein	AA position In Polyprotein	Similarity%
p17_19_28	IRLRPGGKKK	IRLRPGGKKK	p17	19-28	Gag	19-28	100.0
p17_p24	VSQNYPIVQN	VSQNYPIVQN	-	-	Gag	128-137	100.0