BLAST processing rules

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HSP Processing: NCBI BLAST 1.4 series and WU-BLAST 2.0 series

The rules used in MView for selecting and tiling HSPs. The command line option -hsp mode is used to choose between ranked (the default), all, or discrete processing.

BLASTP
Input		Output		Orient		Assemble	Renumber	Filter
qry	hit	qry	hit	qry	hit
pro	pro	pro	pro	+	+	simple	no	none
-hsp ranked		For each ranked hit, HSPs corresponding to those in the ranking are selected for assembly having: (i) same-sized fragment set 'N', (ii) same p-value 'P'. Row data fields: (i) rank as integral 'hitnum', (ii) identifier, (iii) description, (iv) ranked 'score', (v) ranked 'P(N)', (vi) ranked 'N'.
-hsp all		For each ranked hit, all HSPs are selected for assembly. Row data fields: (i) rank as integral 'hitnum', (ii) identifier, (iii) description, (iv) highest 'score', (v) lowest 'P', (vi) total number of HSPs 'N'.
-hsp discrete		For each ranked hit, every HSP is assigned its own row. Row data fields: (i) HSP rank as compound rank 'hitnum.alignmentnum', (ii) identifier, (iii) description, (iv) HSP 'score', (v) HSP 'P', (vi) 'N'=1.
BLASTN
Input		Output		Orient		Assemble	Renumber	Filter
qry	hit	qry	hit	qry	hit
dna	dna	dna	dna	+	+	simple	no	query orient
				+	-	simple	no	query orient
				-	+	reverse	no	query orient
				-	-	reverse	no	query orient
For a given query orientation (+, -):
-hsp ranked		For each ranked hit, HSPs corresponding to those in the ranking are selected for assembly having: (i) same-sized fragment set 'N', (ii) same p-value 'P', (iii) same hit orientation. Row data fields: (i) rank as integral 'hitnum', (ii) identifier, (iii) description, (iv) ranked 'score', (v) ranked 'P(N)', (vi) ranked 'N', (vii) 'hit' orientation.
-hsp all		For each ranked hit, HSPs are selected for assembly having: (i) same hit orientation. Row data fields: (i) rank as compound 'hitnum.alignmentnum', (ii) identifier, (iii) description, (iv) highest 'score', (v) lowest 'P', (vi) total number of HSPs 'N', (vii) 'hit' orientation.
-hsp discrete		For each ranked hit, every HSP is assigned its own row. Row data fields: (i) HSP rank as compound rank 'hitnum.alignmentnum', (ii) identifier, (iii) description, (iv) HSP 'score', (v) HSP 'P', (vi) 'N'=1, (vii) 'hit' orientation.
BLASTX
Input		Output		Orient		Assemble	Renumber	Filter
qry	hit	qry	hit	qry	hit
dna	pro	pro	pro	+F	+	simple	yes	query orient
				-F	+	reverse	yes	query orient
For a given query orientation (+, -) derived from the query reading frame 'F':
-hsp ranked		For each ranked hit, HSPs corresponding to those in the ranking are selected for assembly having: (i) same-sized fragment set 'N', (ii) same p-value 'P', (iii) same query orientation. Row data fields: (i) rank as integral 'hitnum', (ii) identifier, (iii) description, (iv) ranked 'score', (v) ranked 'P(N)', (vi) ranked 'N', (vii) query orientation 'qry'.
-hsp all		For each ranked hit, HSPs are selected for assembly having: (i) same query orientation. Row data fields: (i) rank as integral 'hitnum', (ii) identifier, (iii) description, (iv) highest 'score', (v) lowest 'P', (vi) total number of HSPs 'N', (vii) query orientation 'qry'.
-hsp discrete		For each ranked hit, every HSP is assigned its own row. Row data fields: (i) HSP rank as compound rank 'hitnum.alignmentnum', (ii) identifier, (iii) description, (iv) HSP 'score', (v) HSP 'P', (vi) 'N'=1, (vii) query orientation 'qry'.
TBLASTN
Input		Output		Orient		Assemble	Renumber	Filter
qry	hit	qry	hit	qry	hit
pro	dna	pro	pro	+	+F	simple	no	none
				+	-F	simple	no	none
-hsp ranked		For each ranked hit, HSPs corresponding to those in the ranking are selected for assembly having: (i) same-sized fragment set 'N', (ii) same p-value 'P', (iii) same hit orientation. Row data fields: (i) rank as integral 'hitnum', (ii) identifier, (iii) description, (iv) ranked 'score', (v) ranked 'P(N)', (vi) ranked 'N', (vii) 'hit' orientation.
-hsp all		For each ranked hit, HSPs are selected for assembly having: (i) same hit orientation. Row data fields: (i) rank as compound 'hitnum.alignmentnum', (ii) identifier, (iii) description, (iv) highest 'score', (v) lowest 'P', (vi) total number of HSPs 'N', (vii) 'hit' orientation.
-hsp discrete		For each ranked hit, every HSP is assigned its own row. Row data fields: (i) HSP rank as compound rank 'hitnum.alignmentnum', (ii) identifier, (iii) description, (iv) HSP 'score', (v) HSP 'P', (vi) 'N'=1, (vii) 'hit' orientation.
TBLASTX
Input		Output		Orient		Assemble	Renumber	Filter
qry	hit	qry	hit	qry	hit
dna	dna	pro	pro	+F	+F	simple	yes	query orient
				+F	-F	simple	yes	query orient
				-F	+F	reverse	yes	query orient
				-F	-F	reverse	yes	query orient
For a given query orientation (+, -) derived from the query reading frame 'F':
-hsp ranked		For each ranked hit, HSPs corresponding to those in the ranking are selected for assembly having: (i) same-sized fragment set 'N', (ii) same p-value 'P', (iii) same hit orientation. Row data fields: (i) rank as integral 'hitnum', (ii) identifier, (iii) description, (iv) ranked 'score', (v) ranked 'P(N)', (vi) ranked 'N', (vii) 'hit' orientation.
-hsp all		For each ranked hit, HSPs are selected for assembly having: (i) same hit orientation. Row data fields: (i) rank as compound 'hitnum.alignmentnum', (ii) identifier, (iii) description, (iv) highest 'score', (v) lowest 'P', (vi) total number of HSPs 'N', (vii) 'hit' orientation.
-hsp discrete		For each ranked hit, every HSP is assigned its own row. Row data fields: (i) HSP rank as compound rank 'hitnum.alignmentnum', (ii) identifier, (iii) description, (iv) HSP 'score', (v) HSP 'P', (vi) 'N'=1, (vii) 'hit' orientation.

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