BlastPShortParams (BioFSharp)

BlastP.BlastPShortParams Type

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

DSL fo the blastp 'blastp-short' task command line options blastp-short is optimized for query sequences shorter than 30 residues

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 1: Composition-based statistics as in NAR 29:2994-3005, 2001 2 or T or t : Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties 3: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally Item : `string`
`DBHardMask int` Full Usage: `DBHardMask int` Parameters: Item : `int`	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`	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`
`Threshold int` Full Usage: `Threshold int` Parameters: Item : `int`	thresholdMinimum score to add a word to the BLAST lookup table. Item : `int`
`UseSWTback` Full Usage: `UseSWTback`	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. Item : `int`
`XDropGapFinal float` Full Usage: `XDropGapFinal float` Parameters: Item : `float`	Heuristic value (in bits) for final gapped alignment/ Item : `float`

Static members

Static member Description

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


                
                  
                    
                      BlastPShortParams.makeCmd

Full Usage: BlastPShortParams.makeCmd

Returns: BlastPShortParams -> string list

Returns: BlastPShortParams -> string list


                
                  
                    
                      BlastPShortParams.makeCmdWith m

Full Usage: BlastPShortParams.makeCmdWith m

Parameters:

m : MountInfo

Returns: BlastPShortParams -> string list

m : MountInfo

Returns: BlastPShortParams -> string list