HIP2: HAPTIC3/HEPTAD2 Input Preprocessor

Use HIP2 to prepare input sequence data for HAPTIC3 and HEPTAD2.

Minimum excluded hydrophobic residue (ACFILMV) run length:
Minimum excluded order-promoting residue (CFHILMNVWY) run length:
Strongly disorder-promoting (PKRED/end) residue fraction window width:
Strongly disorder-promoting (PKRED/end) residue fraction cutoff value:

Excluded amino-acid residue/s:
A (ALA)	C (CYS)	D (ASP)	E (GLU)	F (PHE)
G (GLY)	H (HIS)	I (ILE)	K (LYS)	L (LEU)
M (MET)	N (ASN)	P (PRO)	Q (GLN)	R (ARG)
S (SER)	T (THR)	V (VAL)	W (TRP)	Y (TYR)

Excluded amino-acid residue/s in sequence motifs:

Glycosylated N in NXS or NXT where X is any residue except P

Input peptidic sequence data (FASTA format):

Notes:

Minimum excluded hydrophobic residue (ACFILMV) run length is the size of the smallest hydrophobic blob whose residues are deemed inaccessible for binding by paratopes.
Minimum excluded order-promoting residue (CFHILMNVWY) run length is the size of the shortest ordered sequence segment whose residues are deemed inaccessible for binding by paratopes.
Strongly disorder-promoting residues are proline (P) and/or bear formal charge/s (KRED and/or at N- or C-terminal/end position), so sequence segments of length equal to window width whose fraction of such residues is less than cutoff value are deemed inaccessible for binding by paratopes.
Excluded amino-acid residues may be those deemed problematic in view of chemical reactivity (e.g., susceptibility to oxidative damage, as in the case of methionine).
Canonical N-glycosylation of asparagine is expected only for surface and secreted protein antigens of eukaryotes (versus prokaryotes).
HIP2 output represents excluded residues using lower-case single-letter codes (e.g., 'a' versus 'A'), which are neglected by HAPTIC3 and HEPTAD2 for generation of candidate epitopes.