MegablastParams (BioFSharp)

BlastN.MegablastParams Type

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

DSL fo the blastn 'megablast' task command line options megablast is usually used for very similar sequences (e.g, sequencing errors)

Union cases

Union case	Description
`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`
`Dust string` Full Usage: `Dust string` Parameters: Item : `string`	Filter query sequence with dust. Item : `string`
`FilteringDB string` Full Usage: `FilteringDB string` Parameters: Item : `string`	Mask query using the sequences in this database. Item : `string`
`GapExtend int` Full Usage: `GapExtend int` Parameters: Item : `int`	gapextend Item : `int`
`GapOpen int` Full Usage: `GapOpen int` Parameters: Item : `int`	Cost to open a gap. See appendix “BLASTN reward/penalty values”. Item : `int`
`IndexName string` Full Usage: `IndexName string` Parameters: Item : `string`	MegaBLAST database index name. Item : `string`
`LowerCaseMasking` Full Usage: `LowerCaseMasking`	Use lower case filtering in query and subject sequence(s).
`MinRawGappedScore int` Full Usage: `MinRawGappedScore int` Parameters: Item : `int`	Minimum raw gapped score to keep an alignment in the preliminary gapped and trace-back stages. Normally set based upon expect value. Item : `int`
`NoGreedy` Full Usage: `NoGreedy`	Use non-greedy dynamic programming extension.
`Penalty int` Full Usage: `Penalty int` Parameters: Item : `int`	Penalty for a nucleotide mismatch. Item : `int`
`PercIdentity int` Full Usage: `PercIdentity int` Parameters: Item : `int`	Percent identity cutoff. Item : `int`
`Reward int` Full Usage: `Reward int` Parameters: Item : `int`	Reward for a nucleotide match. Item : `int`
`SoftMasking bool` Full Usage: `SoftMasking bool` Parameters: Item : `bool`	Apply filtering locations as soft masks (i.e., only for finding initial matches). Item : `bool`
`Strand string` Full Usage: `Strand string` Parameters: Item : `string`	Query strand(s) to search against database/subject. Choice of both, minus, or plus. Item : `string`
`Ungapped` Full Usage: `Ungapped`	Perform ungapped alignment.
`UseIndex bool` Full Usage: `UseIndex bool` Parameters: Item : `bool`	Use MegaBLAST database index. Indices may be created with the makembindex application. Item : `bool`
`WindowMaskerDB string` Full Usage: `WindowMaskerDB string` Parameters: Item : `string`	Enable WindowMasker filtering using this file. Item : `string`
`WindowMaskerTaxId int` Full Usage: `WindowMaskerTaxId int` Parameters: Item : `int`	Enable WindowMasker filtering using a Taxonomic ID. Item : `int`
`WordSize int` Full Usage: `WordSize int` Parameters: Item : `int`	Length of initial exact match. Item : `int`
`XDropGap float` Full Usage: `XDropGap float` Parameters: Item : `float`	Heuristic value (in bits) for preliminary gapped extensions. Item : `float`
`XDropGapFinal float` Full Usage: `XDropGapFinal float` Parameters: Item : `float`	Heuristic value (in bits) for final gapped alignment. Item : `float`
`XDropUngap float` Full Usage: `XDropUngap float` Parameters: Item : `float`	Heuristic value (in bits) for ungapped extensions. Item : `float`

Static members

Static member Description

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


                
                  
                    
                      MegablastParams.makeCmd

Full Usage: MegablastParams.makeCmd

Returns: MegablastParams -> string list

Returns: MegablastParams -> string list


                
                  
                    
                      MegablastParams.makeCmdWith m

Full Usage: MegablastParams.makeCmdWith m

Parameters:

m : MountInfo

Returns: MegablastParams -> string list

m : MountInfo

Returns: MegablastParams -> string list