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.