NCBI BLAST series 2 and NCBI BLAST+¶

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

NCBI BLAST series 2 (including PSI-BLAST)
NCBI BLAST+

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, alignments corresponding to those in the ranking are selected for assembly having: (i) same expectation, E, (ii) same score, bits. Row data fields: (i) rank as integral hitnum, (ii) identifier, (iii) description, (iv) ranked bits, (v) ranked E, (vi) N=1, (vii) hit orientation.

-hsp all

For each ranked hit, all alignments are selected for assembly. Row data fields: (i) rank as integral hitnum, (ii) identifier, (iii) description, (iv) highest bits, (v) lowest E, (vi) total number of alignments N.

-hsp discrete

For each ranked hit, every alignment is assigned its own row. Row data fields: (i) alignment rank as compound rank hitnum.alignum, (ii) identifier, (iii) description, (iv) alignment bits, (v) alignment E, (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

none

dna

dna

dna

dna

+

--

forward

no

none

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

MView option

Description

-hsp ranked

For each ranked hit, alignments corresponding to those in the ranking are selected for assembly having: (i) same expectation, E, (ii) same score, bits. Row data fields: (i) rank as integral hitnum, (ii) identifier, (iii) description, (iv) ranked bits, (v) ranked E, (vi) N=1, (vii) hit orientation.

-hsp all

For each ranked hit, alignments are selected for assembly having: (i) same hit orientation. Row data fields: (i) rank as compound hitnum.alignum, (ii) identifier, (iii) description, (iv) highest bits, (v) lowest E, (vi) total number of alignments N, (vii) hit orientation.

-hsp discrete

For each ranked hit, every alignment is assigned its own row. Row data fields: (i) alignment rank as compound rank hitnum.alignum, (ii) identifier, (iii) description, (iv) alignment bits, (v) alignment E, (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

+

+

forward

yes

query orient

dna

pro

pro

pro

--

+

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, alignments corresponding to those in the ranking are selected for assembly having: (i) same expectation, E, (ii) same score, bits, (iii) same query orientation. Row data fields: (i) rank as integral hitnum, (ii) identifier, (iii) description, (iv) ranked bits, (v) ranked E, (vi) N=1, (vii) query orientation.

-hsp all

For each ranked hit, alignments are selected for assembly having: (i) same query orientation. Row data fields: (i) rank as integral hitnum, (ii) identifier, (iii) description, (iv) highest bits, (v) lowest E, (vi) total number of alignments, N, (vii) query orientation.

-hsp discrete

For each ranked hit, every alignment is assigned its own row. Row data fields: (i) alignment rank as compound rank hitnum.alignum, (ii) identifier, (iii) description, (iv) alignment bits, (v) alignment E, (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

+

+

forward

no

none

pro

dna

pro

pro

+

--

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, alignments corresponding to those in the ranking are selected for assembly having: (i) same expectation, E, (ii) same score, bits, (iii) same hit orientation. Row data fields: (i) rank as integral hitnum, (ii) identifier, (iii) description, (iv) ranked bits, (v) ranked E, (vi) N=1, (vii) hit orientation.

-hsp all

For each ranked hit, alignments are selected for assembly having: (i) same hit orientation. Row data fields: (i) rank as compound hitnum.alignum, (ii) identifier, (iii) description, (iv) highest bits, (v) lowest E, (vi) total number of alignments, N, (vii) hit orientation.

-hsp discrete

For each ranked hit, every alignment is assigned its own row. Row data fields: (i) alignment rank as compound rank hitnum.alignum, (ii) identifier, (iii) description, (iv) alignment bits, (v) alignment E, (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

+

+

forward

yes

query orient

dna

dna

pro

pro

+

--

forward

yes

query orient

dna

dna

pro

pro

--

+

reverse

yes

query orient

dna

dna

pro

pro

--

--

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, alignments corresponding to those in the ranking are selected for assembly having: (i) same expectation, E, (ii) same score, bits, (iii) same hit orientation. Row data fields: (i) rank as integral hitnum, (ii) identifier, (iii) description, (iv) ranked bits, (v) ranked E, (vi) N=1, (vii) hit orientation.

-hsp all

For each ranked hit, alignments are selected for assembly having: (i) same hit orientation. Row data fields: (i) rank as compound hitnum.alignum, (ii) identifier, (iii) description, (iv) highest bits, (v) lowest E, (vi) total number of alignments, N, (vii) hit orientation.

-hsp discrete

For each ranked hit, every alignment is assigned its own row. Row data fields: (i) alignment rank as compound rank hitnum.alignum, (ii) identifier, (iii) description, (iv) alignment bits, (v) alignment E, (vi) N=1, (vii) hit orientation.

PSI-BLAST¶

Iteratively searches a protein query sequence against a protein sequence database. PSI-BLAST output is processed as a sequence of BLASTP cycles.

Input

Output

Orient

Assemble

Renumber

Filter

qry

hit

qry

hit

qry

hit

pro

pro

pro

pro

+

+

forward

no

cycle

BLASTP and PSI-BLAST share the same HSP processing rules. The query orientation is always ‘+’ giving one alignment per cycle.

MView option

Description

-hsp ranked

For each ranked hit, the first alignment is selected to form an alignment row using: (i) same expectation, E, (ii) same score, bits. Row data fields: (i) rank as integral hitnum, (ii) identifier, (iii) description, (iv) ranked bits, (v) ranked E, (vi) N=1.

-hsp all

For each ranked hit, all alignments are selected for assembly. Row data fields: (i) rank as integral hitnum, (ii) identifier, (iii) description, (iv) highest bits, (v) lowest E, (vi) total number of alignments N.

-hsp discrete

For each ranked hit, every alignment is assigned its own row. Row data fields: (i) alignment rank as compound rank hitnum.alignum, (ii) identifier, (iii) description, (iv) alignment bits, (v) alignment E, (vi) N=1.

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 PSI-BLAST search cycle, 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. BLAST series 2 onwards produces gapped alignments by default rather than separate HSPs so N=1.

E

Expectation or e-value: the expected number of hits by chance.

bits

NCBI BLAST 2.0 hit ranking rounds HSP scores which are floating point to the nearset integer, so MView takes this into account when selecting HSPs.

NCBI BLAST series 2 and NCBI BLAST+¶

BLASTP¶

BLASTN¶

BLASTX¶

TBLASTN¶

TBLASTX¶

PSI-BLAST¶

Column headings¶

Key¶

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MView option	Description
`-hsp ranked`	For each ranked hit, alignments corresponding to those in the ranking are selected for assembly having: (i) same expectation, E, (ii) same score, bits. Row data fields: (i) rank as integral hitnum, (ii) identifier, (iii) description, (iv) ranked bits, (v) ranked E, (vi) N=1, (vii) hit orientation.
`-hsp all`	For each ranked hit, all alignments are selected for assembly. Row data fields: (i) rank as integral hitnum, (ii) identifier, (iii) description, (iv) highest bits, (v) lowest E, (vi) total number of alignments N.
`-hsp discrete`	For each ranked hit, every alignment is assigned its own row. Row data fields: (i) alignment rank as compound rank hitnum.alignum, (ii) identifier, (iii) description, (iv) alignment bits, (v) alignment E, (vi) N=1.

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

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

MView option	Description
`-hsp ranked`	For each ranked hit, the first alignment is selected to form an alignment row using: (i) same expectation, E, (ii) same score, bits. Row data fields: (i) rank as integral hitnum, (ii) identifier, (iii) description, (iv) ranked bits, (v) ranked E, (vi) N=1.
`-hsp all`	For each ranked hit, all alignments are selected for assembly. Row data fields: (i) rank as integral hitnum, (ii) identifier, (iii) description, (iv) highest bits, (v) lowest E, (vi) total number of alignments N.
`-hsp discrete`	For each ranked hit, every alignment is assigned its own row. Row data fields: (i) alignment rank as compound rank hitnum.alignum, (ii) identifier, (iii) description, (iv) alignment bits, (v) alignment E, (vi) N=1.

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 PSI-BLAST search cycle, BLASTN query strand orientation, etc.

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. BLAST series 2 onwards produces gapped alignments by default rather than separate HSPs so N=1.
E	Expectation or e-value: the expected number of hits by chance.
bits	NCBI BLAST 2.0 hit ranking rounds HSP scores which are floating point to the nearset integer, so MView takes this into account when selecting HSPs.