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.
| Program | Input | Output | Orient | Assemble | Renumber | Filter | |||
|---|---|---|---|---|---|---|---|---|---|
| qry | hit | qry | hit | qry | hit | ||||
| BLASTP | pro | pro | pro | pro | + | + | simple | no | none |
| HSP processing modes | |||||||||
| ranked | For each ranked hit, HSPs corresponding to those in the ranking are selected for assembly having: 1) same-sized fragment set 'N', 2) same p-value 'P'. Row data fields: 1) rank as integral 'hitnum', 2) identifier, 3) description, 4) ranked 'score', 5) ranked 'P(N)', 6) ranked 'N'. | ||||||||
| all | For each ranked hit, all HSPs are selected for assembly. Row data fields: 1) rank as integral 'hitnum', 2) identifier, 3) description, 4) highest 'score', 5) lowest 'P', 6) total number of HSPs 'N'. | ||||||||
| discrete | For each ranked hit, every HSP is assigned its own row. Row data fields: 1) HSP rank as compound rank 'hitnum.alignmentnum', 2) identifier, 3) description, 4) HSP 'score', 5) HSP 'P', 6) 'N'=1. | ||||||||
| Program | Input | Output | Orient | Assemble | Renumber | Filter | |||
| qry | hit | qry | hit | qry | hit | ||||
| BLASTN | dna | dna | dna | dna | + | + | simple | no | query sign |
| + | - | simple | no | query sign | |||||
| - | + | reverse | no | query sign | |||||
| - | - | reverse | no | query sign | |||||
| HSP processing modes | |||||||||
| For a given query orientation (+, -): | |||||||||
| ranked | For each ranked hit, HSPs corresponding to those in the ranking are selected for assembly having: 1) same-sized fragment set 'N', 2) same p-value 'P', 3) same hit orientation. Row data fields: 1) rank as integral 'hitnum', 2) identifier, 3) description, 4) ranked 'score', 5) ranked 'P(N)', 6) ranked 'N', 7) 'hit' orientation. | ||||||||
| all | For each ranked hit, HSPs are selected for assembly having: 1) same hit orientation. Row data fields: 1) rank as compound 'hitnum.alignmentnum', 2) identifier, 3) description, 4) highest 'score', 5) lowest 'P', 6) total number of HSPs 'N', 7) 'hit' orientation. | ||||||||
| discrete | For each ranked hit, every HSP is assigned its own row. Row data fields: 1) HSP rank as compound rank 'hitnum.alignmentnum', 2) identifier, 3) description, 4) HSP 'score', 5) HSP 'P', 6) 'N'=1, 7) 'hit' orientation. | ||||||||
| Program | Input | Output | Orient | Assemble | Renumber | Filter | |||
| qry | hit | qry | hit | qry | hit | ||||
| BLASTX | dna | pro | pro | pro | +F | + | simple | yes | query sign |
| -F | + | reverse | yes | query sign | |||||
| HSP processing modes | |||||||||
| For a given query orientation (+, -) derived from the query reading frame 'F': | |||||||||
| ranked | For each ranked hit, HSPs corresponding to those in the ranking are selected for assembly having: 1) same-sized fragment set 'N', 2) same p-value 'P', 3) same query orientation. Row data fields: 1) rank as integral 'hitnum', 2) identifier, 3) description, 4) ranked 'score', 5) ranked 'P(N)', 6) ranked 'N', 7) query orientation 'qry'. | ||||||||
| all | For each ranked hit, HSPs are selected for assembly having: 1) same query orientation. Row data fields: 1) rank as integral 'hitnum', 2) identifier, 3) description, 4) highest 'score', 5) lowest 'P', 6) total number of HSPs 'N', 7) query orientation 'qry'. | ||||||||
| discrete | For each ranked hit, every HSP is assigned its own row. Row data fields: 1) HSP rank as compound rank 'hitnum.alignmentnum', 2) identifier, 3) description, 4) HSP 'score', 5) HSP 'P', 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 | + | +F | simple | no | none |
| + | -F | simple | no | none | |||||
| HSP processing modes | |||||||||
| ranked | For each ranked hit, HSPs corresponding to those in the ranking are selected for assembly having: 1) same-sized fragment set 'N', 2) same p-value 'P', 3) same hit orientation. Row data fields: 1) rank as integral 'hitnum', 2) identifier, 3) description, 4) ranked 'score', 5) ranked 'P(N)', 6) ranked 'N', 7) 'hit' orientation. | ||||||||
| all | For each ranked hit, HSPs are selected for assembly having: 1) same hit orientation. Row data fields: 1) rank as compound 'hitnum.alignmentnum', 2) identifier, 3) description, 4) highest 'score', 5) lowest 'P', 6) total number of HSPs 'N', 7) 'hit' orientation. | ||||||||
| discrete | For each ranked hit, every HSP is assigned its own row. Row data fields: 1) HSP rank as compound rank 'hitnum.alignmentnum', 2) identifier, 3) description, 4) HSP 'score', 5) HSP 'P', 6) 'N'=1, 7) 'hit' orientation. | ||||||||
| Program | Input | Output | Orient | Assemble | Renumber | Filter | |||
| qry | hit | qry | hit | qry | hit | ||||
| TBLASTX | dna | dna | pro | pro | +F | +F | simple | yes | query sign |
| +F | -F | simple | yes | query sign | |||||
| -F | +F | reverse | yes | query sign | |||||
| -F | -F | reverse | yes | query sign | |||||
| HSP processing modes | |||||||||
| For a given query orientation (+, -) derived from the query reading frame 'F': | |||||||||
| ranked | For each ranked hit, HSPs corresponding to those in the ranking are selected for assembly having: 1) same-sized fragment set 'N', 2) same p-value 'P', 3) same hit orientation. Row data fields: 1) rank as integral 'hitnum', 2) identifier, 3) description, 4) ranked 'score', 5) ranked 'P(N)', 6) ranked 'N', 7) 'hit' orientation. | ||||||||
| all | For each ranked hit, HSPs are selected for assembly having: 1) same hit orientation. Row data fields: 1) rank as compound 'hitnum.alignmentnum', 2) identifier, 3) description, 4) highest 'score', 5) lowest 'P', 6) total number of HSPs 'N', 7) 'hit' orientation. | ||||||||
| discrete | For each ranked hit, every HSP is assigned its own row. Row data fields: 1) HSP rank as compound rank 'hitnum.alignmentnum', 2) identifier, 3) description, 4) HSP 'score', 5) HSP 'P', 6) 'N'=1, 7) 'hit' orientation. | ||||||||