NCBI BLAST 2.0 series and PSI-BLAST

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.

In the BLAST 2.0 series MView assumes that only one fragment (a gapped alignment) is required in 'ranked' mode and accepts the FIRST alignment with score and expectation matching those in the hit ranking.

Differences between NCBI BLAST 1.4 and NCBI BLAST 2.0

• In gapped mode, the BLAST 2.0 programs produce no 'N' fragment counts.
• Significances are reported only as Expectation (e-values) 'E' rather than p-values 'P'.
• BLASTN: negative orientation query strands are not reported because the query and hit can always be reverse complemented to revert the query back to the positive strand orientation.
• BLASTX: query strands don't carry frame information.
• TBLASTN: hit strands don't carry frame information.
• TBLASTX: query and hit strands don't carry frame information.

Program	Input		Output		Orient		Assemble	Renumber	Filter
	qry	hit	qry	hit	qry	hit
BLASTP	pro	pro	pro	pro	+	+	simple	no	none
PSI-BLAST	pro	pro	pro	pro	+	+	simple	no	cycle
HSP processing modes
For each specified search cycle (PSI-BLAST only):
ranked	For each ranked hit, the first alignment is selected to form an alignment row using: 1) same expectation 'E', 2) same score 'bits'. Row data fields: 1) rank as integral 'hitnum', 2) identifier, 3) description, 4) ranked 'bits', 5) ranked 'E', 6) 'N'=1.
all	For each ranked hit, all alignments are selected for assembly. Row data fields: 1) rank as integral 'hitnum', 2) identifier, 3) description, 4) highest 'bits', 5) lowest 'E', 6) total number of alignments 'N'.
discrete	For each ranked hit, every alignment is assigned its own row. Row data fields: 1) alignment rank as compound rank 'hitnum.alignmentnum', 2) identifier, 3) description, 4) alignment 'bits', 5) alignment 'E', 6) 'N'=1.
Program	Input		Output		Orient		Assemble	Renumber	Filter
	qry	hit	qry	hit	qry	hit
BLASTN	dna	dna	dna	dna	+	+	simple	no	none
					+	-	simple	no	none
HSP processing modes
For a given query orientation (+, -) derived from the query sequence numbering:
ranked	For each ranked hit, alignments corresponding to those in the ranking are selected for assembly having: 1) same expectation 'E', 2) same score 'bits'. Row data fields: 1) rank as integral 'hitnum', 2) identifier, 3) description, 4) ranked 'bits', 5) ranked 'E', 6) 'N'=1. 7) 'hit' orientation.
all	For each ranked hit, alignments are selected for assembly having: 1) same hit orientation. Row data fields: 1) rank as compound 'hitnum.alignmentnum', 2) identifier, 3) description, 4) highest 'bits', 5) lowest 'E', 6) total number of alignments 'N', 7) 'hit' orientation.
discrete	For each ranked hit, every alignment is assigned its own row. Row data fields: 1) alignment rank as compound rank 'hitnum.alignmentnum', 2) identifier, 3) description, 4) alignment 'bits', 5) alignment 'E', 6) 'N'=1, 7) 'hit' orientation.
Program	Input		Output		Orient		Assemble	Renumber	Filter
	qry	hit	qry	hit	qry	hit
BLASTX	dna	pro	pro	pro	+	+	simple	yes	query sign
					-	+	reverse	yes	query sign
HSP processing modes
For a given query orientation (+, -) derived from the query sequence numbering:
ranked	For each ranked hit, alignments corresponding to those in the ranking are selected for assembly having: 1) same expectation 'E', 2) same score 'bits', 3) same query orientation. Row data fields: 1) rank as integral 'hitnum', 2) identifier, 3) description, 4) ranked 'bits', 5) ranked 'E', 6) 'N=1', 7) query orientation 'qry'.
all	For each ranked hit, alignments are selected for assembly having: 1) same query orientation. Row data fields: 1) rank as integral 'hitnum', 2) identifier, 3) description, 4) highest 'bits', 5) lowest 'E', 6) total number of alignments 'N', 7) query orientation 'qry'.
discrete	For each ranked hit, every alignment is assigned its own row. Row data fields: 1) alignment rank as compound rank 'hitnum.alignmentnum', 2) identifier, 3) description, 4) alignment 'bits', 5) alignment 'E', 6) 'N'=1, 7) query orientation 'qry'.
Program	Input		Output		Orient		Assemble	Renumber	Filter
	qry	hit	qry	hit	qry	hit
TBLASTN	pro	dna	pro	pro	+	+	simple	no	none
					+	-	simple	no	none
HSP processing modes
ranked	For each ranked hit, alignments corresponding to those in the ranking are selected for assembly having: 1) same expectation 'E', 2) same score 'bits', 3) same hit orientation. Row data fields: 1) rank as integral 'hitnum', 2) identifier, 3) description, 4) ranked 'bits', 5) ranked 'E', 'N'=1, 7) 'hit' orientation.
all	For each ranked hit, alignments are selected for assembly having: 1) same hit orientation. Row data fields: 1) rank as compound 'hitnum.alignmentnum', 2) identifier, 3) description, 4) highest 'bits', 5) lowest 'E', 6) total number of alignments 'N', 7) 'hit' orientation.
discrete	For each ranked hit, every alignment is assigned its own row. Row data fields: 1) alignment rank as compound rank 'hitnum.alignmentnum', 2) identifier, 3) description, 4) alignment 'bits', 5) alignment 'E', 6) 'N'=1, 7) 'hit' orientation.
Program	Input		Output		Orient		Assemble	Renumber	Filter
	qry	hit	qry	hit	qry	hit
TBLASTX	dna	dna	pro	pro	+	+	simple	yes	query sign
					+	-	simple	yes	query sign
					-	+	reverse	yes	query sign
					-	-	reverse	yes	query sign
HSP processing modes
For a given query orientation (+, -) derived from the query sequence numbering:
ranked	For each ranked hit, alignments corresponding to those in the ranking are selected for assembly having: 1) same expectation 'E', 2) same score 'bits', 3) same hit orientation. Row data fields: 1) rank as integral 'hitnum', 2) identifier, 3) description, 4) ranked 'bits', 5) ranked 'E', 6) 'N'=1, 7) 'hit' orientation.
all	For each ranked hit, alignments are selected for assembly having: 1) same hit orientation. Row data fields: 1) rank as compound 'hitnum.alignmentnum', 2) identifier, 3) description, 4) highest 'bits', 5) lowest 'E', 6) total number of alignments 'N', 7) 'hit' orientation.
discrete	For each ranked hit, every alignment is assigned its own row. Row data fields: 1) alignment rank as compound rank 'hitnum.alignmentnum', 2) identifier, 3) description, 4) alignment 'bits', 5) alignment 'E', 6) 'N'=1, 7) 'hit' orientation.