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.