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Matrix families versus individual matrices

Searching transcription factor binding sites for NFkappaB in a HIV-1 long terminal repeat sequence (HIVTH475A) yields the following results:

- Using parameter settings "individual matrices"

Inspecting sequence hivth475a [L31963] (1 - 672):

	Family/matrix	Opt.	Position		Str.	Core sim.	Matrix sim.	Sequence
			from - to	anchor
	V$NFKB/NFKAPPAB.01	0.88	345 - 359	352	(+)	1.000	0.988	aaGGGActttccgct
	V$NFKB/NFKAPPAB65.01	0.87	345 - 359	352	(+)	1.000	0.984	aagggactTTCCgct
	V$NFKB/NFKAPPAB.02	0.81	345 - 359	352	(+)	1.000	0.977	aaGGGActttccgct
	V$NFKB/NFKAPPAB.03	0.84	345 - 359	352	(+)	1.000	0.968	aaGGGActttccgct
	V$NFKB/NFKAPPAB.02	0.81	359 - 373	366	(+)	1.000	1.000	tgGGGActttccagg
	V$NFKB/NFKAPPAB.01	0.88	359 - 373	366	(+)	1.000	0.988	tgGGGActttccagg
	V$NFKB/NFKAPPAB65.01	0.87	359 - 373	366	(+)	1.000	0.984	tggggactTTCCagg
	V$NFKB/NFKAPPAB.03	0.84	359 - 373	366	(+)	1.000	0.994	tgGGGActttccagg
	V$NFKB/NFKAPPAB.03	0.84	385 - 399	392	(+)	1.000	0.845	tgGGGAactttccgc
	V$NFKB/NFKAPPAB.03	0.84	386 - 400	393	(+)	0.775	0.893	ggGGAActttccgct
	V$NFKB/NFKAPPAB.02	0.81	400 - 414	407	(+)	1.000	1.000	tgGGGActttccagg
	V$NFKB/NFKAPPAB.01	0.88	400 - 414	407	(+)	1.000	0.988	tgGGGActttccagg
	V$NFKB/NFKAPPAB65.01	0.87	400 - 414	407	(+)	1.000	0.984	tggggactTTCCagg
	V$NFKB/NFKAPPAB.03	0.84	400 - 414	407	(+)	1.000	0.994	tgGGGActttccagg

• All 5 matrices available for NFkappaB in the MatInspector library (V$NFKAPPAB.01, V$NFKAPPAB.02, V$NFKAPPAB.03, V$NFKAPPAB50.01, V$NFKAPPAB65.01) were selected.
  
• This results in 14 NFkappaB matches (4 distinct matches).

- With matrix families

Inspecting sequence hivth475a [L31963] (1 - 672):

	Family/matrix	Opt.	Position		Str.	Core sim.	Matrix sim.	Sequence
			from - to	anchor
	V$NFKB/NFKAPPAB.01	0.88	345 - 359	352	(+)	1.000	0.988	aaGGGActttccgct
	V$NFKB/NFKAPPAB.02	0.81	359 - 373	366	(+)	1.000	1.000	tgGGGActttccagg
	V$NFKB/NFKAPPAB.03	0.84	386 - 400	393	(+)	0.775	0.893	ggGGAActttccgct
	V$NFKB/NFKAPPAB.02	0.81	400 - 414	407	(+)	1.000	1.000	tgGGGActttccagg

• For this search the matrix family V$NFKB was selected.
  
• The family V$NFKB includes the 5 matrices for NFkappaB listed above as well as 1 matrix for the NFkappaB related factor c-Rel (V$CREL.01).
  
• This results in 4 matches for the NFkappaB family, which are all biologically significant matches.
  

This HIV-1 sequence (L31963) containing a 42 bp duplication (including the 2 NFkappaB sites) was published in:

• Neumann, M., Felber, B., K., Kleinschmidt, A., Froese, B., Erfle, V., Pavlakis, G., N., Brack-Werner, R. (1995).
  Restriction of human immunodeficiency virus type 1 production in a human astrocytoma cell line is associated with a cellular block in Rev function.
  J. Virol. 69, 2159-2167.