NCBI BLAST series 1 and WU-BLAST series 2

The rules used in MView for selecting and tiling HSPs for:

• NCBI BLAST series 1

• WU-BLAST series 2

BLASTP

Searches a protein query sequence against a protein sequence database.

Input		Output		Orient		Assemble	Renumber	Filter
qry	hit	qry	hit	qry	hit
pro	pro	pro	pro	+	+	forward	no	none

The query orientation is always ‘+’ giving one alignment.

MView option	Description
-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.alignum, (ii) identifier, (iii) description, (iv) HSP score, (v) HSP P, (vi), N=1.

BLASTN

Searches a nucleotide query sequence against a nucleotide sequence database.

Input		Output		Orient		Assemble	Renumber	Filter
qry	hit	qry	hit	qry	hit
dna	dna	dna	dna	+	+	forward	no	query orient
dna	dna	dna	dna	+	--	forward	no	query orient
dna	dna	dna	dna	--	+	reverse	no	query orient
dna	dna	dna	dna	--	--	reverse	no	query orient

The query orientation can be ‘+’ or ‘--’ giving two distinct alignments.

MView option	Description
-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.alignum, (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.alignum, (ii) identifier, (iii) description, (iv) HSP score, (v) HSP P, (vi) N=1, (vii) hit orientation.

BLASTX

Searches a nucleotide query sequence against a protein sequence database, translating the query in all 6 reading frames.

Input		Output		Orient		Assemble	Renumber	Filter
qry	hit	qry	hit	qry	hit
dna	pro	pro	pro	+F	+	forward	yes	query orient
dna	pro	pro	pro	--F	+	reverse	yes	query orient

The query orientation can be ‘+’ or ‘--’ giving two distinct alignments by orientation. Query reading frames of the same sign are merged unless -hsp discrete is used.

MView option	Description
-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.
-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.
-hsp discrete	For each ranked hit, every HSP is assigned its own row. Row data fields: (i) HSP rank as compound rank hitnum.alignum, (ii) identifier, (iii) description, (iv) HSP score, (v) HSP P, (vi) N=1, (vii) query orientation.

TBLASTN

Searches a protein query sequence against a nucleotide sequence database, translating the hits in all 6 reading frames.

Input		Output		Orient		Assemble	Renumber	Filter
qry	hit	qry	hit	qry	hit
pro	dna	pro	pro	+	+F	forward	no	none
pro	dna	pro	pro	+	--F	forward	no	none

The query orientation is always ‘+’ giving one alignment. Hit reading frames of the same sign are merged unless -hsp discrete is used.

MView option	Description
-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.alignum, (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.alignum, (ii) identifier, (iii) description, (iv) HSP score, (v) HSP P, (vi) N=1, (vii) hit orientation.

TBLASTX

Searches a nucleotide query sequence against a nucleotide sequence database, translating both query and hit in all 6 reading frames.

Input		Output		Orient		Assemble	Renumber	Filter
qry	hit	qry	hit	qry	hit
dna	dna	pro	pro	+F	+F	forward	yes	query orient
dna	dna	pro	pro	+F	--F	forward	yes	query orient
dna	dna	pro	pro	--F	+F	reverse	yes	query orient
dna	dna	pro	pro	--F	--F	reverse	yes	query orient

The query orientation can be ‘+’ or ‘--’ giving two distinct alignments by orientation. Query and hit reading frames of the same sign are merged, respectively, unless -hsp discrete is used.

MView option	Description
-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.alignum, (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.alignum, (ii) identifier, (iii) description, (iv) HSP score, (v) HSP P, (vi) N=1, (vii) hit orientation.

Column headings

Heading	Description
Input	The input sequence types for the query, ‘qry’, and the ‘hit’, sequences which may be protein ‘pro’ or nucleotide ‘dna’.
Output	The output sequence types produced by the search, may be protein ‘pro’ or nucleotide ‘dna’.
Orient	The orientation of the query and hit sequences given as forward ‘+’ or reverse ‘--’ and sometimes with a reading frame number indicated by ‘+F’ or ‘--F’.
Assemble	The sequence fragment assembly algorithm: forward: Given a list of fragments each numbered from low to high along the query strand (i.e., conventional orientation): stack these at these positions along the query template. reverse: Given a list of fragments each numbered from high to low along the query strand (i.e., individually reversed): reverse each fragment, stack onto the template, reverse the template, which recovers the original numbering high to low and preserves intra- and inter-fragment order.
Renumber	Whether the sequence numbering is modified by MView or not. Given a \((start, stop)\) pair in nucleotide units, the corresponding nearest values in amino acid units are given by: \((start\prime, stop\prime) = (int((start+2)/3), int(stop/3))\) This renumbering is applied to each fragment’s positions along its parent query strand to determine the query template positions in amino acid units.
Filter	Separate MView output must be produced for varous BLAST hit properties, such as BLASTN query strand orientation, etc.

Key

Term	Description
hitnum	The ordinal number (starting at 1) of a search hit as encountered in the ranking section of the raw BLAST output.
alignum	The ordinal number (starting at 1) of a single HSP within a given hit (starting afresh with each hit) as encountered in the raw BLAST output.
N	A count of HSPs which is context dependent in MView. In raw BLAST output it is the number of HSPs deemed by BLAST to belong in a coherent set of alignment fragments, but the MView HSP processing options (ranked, all, discrete) change the precise meaning.
P(N)	The BLAST alignment p-value associated with a set of N HSPs.
P	BLAST 1.4 series reports relatively large p-vales in floating point format rather than scientific notation. The original HSP p-value may be rounded to 2 decimal places in the hit ranking, so comparison of these values by MView when selecting HSPs takes this into account, which could lead to over-selection of HSPs on occasion.
score	The BLAST alignment score.

Differences between NCBI BLAST 1 and NCBI BLAST 2

• In the default gapped mode, the BLAST 2 programs produce no N fragment counts. Fragment counts are switched on in BLAST when it is run in ungapped mode using the blastall... -g F command line option.

• Significances are reported only as Expectation (E-values), E rather than p-values, P.

• BLASTX: query strands don’t carry frame information (early versions only).

• TBLASTN: hit strands don’t carry frame information (early versions only).

• TBLASTX: query and hit strands don’t carry frame information (early versions only).

With BLAST 2 series output, 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. If you wish to see the effect of any other HSPs use the -hsp all or -hsp discrete options to MView. This is particularly important if you use BLAST in ungapped mode.