BlastPParams (BioFSharp)

BlastP.BlastPParams Type

Namespace: BioFSharp.BioContainers
Assembly: BioFSharp.BioContainers.dll
Parent Module: BlastP
Base Type: obj
All Interfaces: IEquatable<BlastPParams> , IStructuralEquatable , IComparable<BlastPParams> , IComparable , IStructuralComparable

DSL fo the blastp 'blastp' task command line options blastp is used for standard protein-protein comparisons

Union cases

Union case	Description
`CompBasedStats string` Full Usage: `CompBasedStats string` Parameters: Item : `string`	Use composition-based statistics: D or d: default (equivalent to 2) 0 or F or f: no composition-based statistics 21:902-911, 2005, conditioned on sequence properties3: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally Item : `string`
`DBHardMask int` Full Usage: `DBHardMask int` Parameters: Item : `int`	db_hard_mask all of int none Filtering algorithm ID to apply to the BLAST database as hard mask (i.e., sequence is masked for all phases of search). Item : `int`
`DBSoftMask int` Full Usage: `DBSoftMask int` Parameters: Item : `int`	db_soft_mask all of int none Filtering algorithm ID to apply to the BLAST database as soft mask (i.e., only for finding initial matches). Item : `int`
`GapExtend int` Full Usage: `GapExtend int` Parameters: Item : `int`	Cost to extend a gap. Item : `int`
`GapOpen int` Full Usage: `GapOpen int` Parameters: Item : `int`	Cost to open a gap. Item : `int`
`LowerCaseMasking` Full Usage: `LowerCaseMasking`	Use lower case filtering in query and subject sequence(s).
`Matrix string` Full Usage: `Matrix string` Parameters: Item : `string`	Scoring matrix name. Item : `string`
`Seg string` Full Usage: `Seg string` Parameters: Item : `string`	Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or 'no' to disable). Item : `string`
`SoftMasking bool` Full Usage: `SoftMasking bool` Parameters: Item : `bool`	Apply filtering locations as soft masks (i.e., only for finding initial matches). Item : `bool`
`Threshold int` Full Usage: `Threshold int` Parameters: Item : `int`	Minimum score to add a word to the BLAST lookup table. Item : `int`
`UseSWTback` Full Usage: `UseSWTback`	use_sw_tback all N/A Compute locally optimal Smith-Waterman alignments?
`WindowSize int` Full Usage: `WindowSize int` Parameters: Item : `int`	Multiple hits window size, use 0 to specify 1-hit algorithm. Item : `int`
`WordSize int` Full Usage: `WordSize int` Parameters: Item : `int`	Word size of initial match. Valid word sizes are 2-7. Item : `int`
`XDropGapFinal float` Full Usage: `XDropGapFinal float` Parameters: Item : `float`	xdrop_gap_final all of float 25 Heuristic value (in bits) for final gapped alignment/ Item : `float`

Static members

Static member Description

Static member	Description
`BlastPParams.makeCmd` Full Usage: `BlastPParams.makeCmd` Returns: `BlastPParams -> string list`	Returns: `BlastPParams -> string list`
`BlastPParams.makeCmdWith m` Full Usage: `BlastPParams.makeCmdWith m` Parameters: m : `MountInfo` Returns: `BlastPParams -> string list`	m : `MountInfo` Returns: `BlastPParams -> string list`


                
                  
                    
                      BlastPParams.makeCmd

Full Usage: BlastPParams.makeCmd

Returns: BlastPParams -> string list

Returns: BlastPParams -> string list


                
                  
                    
                      BlastPParams.makeCmdWith m

Full Usage: BlastPParams.makeCmdWith m

Parameters:

m : MountInfo

Returns: BlastPParams -> string list

m : MountInfo

Returns: BlastPParams -> string list