BlastN (BioFSharp)

BlastN Module

Namespace: BioFSharp.BioContainers
Assembly: BioFSharp.BioContainers.dll
Parent Module: Blast

DSL for blastn programs The blastn application searches a nucleotide query against nucleotide subject sequences or a nucleotide database. Four different tasks are supported: 1.) “megablast”, for very similar sequences (e.g, sequencing errors) 2.) “dc-megablast”, typically used for inter-species comparisons 3.) “blastn”, the traditional program used for inter-species comparisons 4.) “blastn-short”, optimized for sequences less than 30 nucleotides.

Types

Type	Description
BlastNParameters	use this type to specify specific and generic command line parameters for the blastn task like this: let myParams = [ BlastNParameters.CommonOptions [...] BlastNParameters.SpecificOptions [...] ]
BlastNParams	DSL fo blastn command line options blastn is the traditional program used for inter-species comparisons
BlastNShortParameters	use this type to specify specific and generic command line parameters for the blastn-short task like this: let myParams = [ BlastNShortParameters.CommonOptions [...] BlastNShortParameters.SpecificOptions [...] ]
BlastNShortParams	DSL fo the blastn 'blastn-short' task command line options blastn-short is optimized for sequences less than 30 nucleotides.
DCMegablastParameters	use this type to specify specific and generic command line parameters for the blastn dc-megablast task like this: let myParams = [ DCMegablastParameters.CommonOptions [...] DCMegablastParameters.SpecificOptions [...] ]
DCMegablastParams	DSL fo the blastn 'dc-megablast' task command line options dc-megablast is typically used for inter-species comparison
MegablastParameters	use this type to specify specific and generic command line parameters for the blastn megablast task like this: let myParams = [ MegablastParameters.CommonOptions [...] MegablastParameters.SpecificOptions [...] ]
MegablastParams	DSL fo the blastn 'megablast' task command line options megablast is usually used for very similar sequences (e.g, sequencing errors)

Functions and values

Function or value	Description
`BlastN.runBlastN bcContext opt` Full Usage: `BlastN.runBlastN bcContext opt` Parameters: bcContext : `BcContext` opt : `BlastNParameters list`	run `blastn -task blastn` in the specified container context with the given commands bcContext : `BcContext` opt : `BlastNParameters list`
`BlastN.runBlastNAsync bcContext opt` Full Usage: `BlastN.runBlastNAsync bcContext opt` Parameters: bcContext : `BcContext` opt : `BlastNParameters list` Returns: `Async<unit>`	returns an asynchronous computation that will run `blastn -task blastn` in the specified container context with the given commands bcContext : `BcContext` opt : `BlastNParameters list` Returns: `Async<unit>`
`BlastN.runBlastNShort bcContext opt` Full Usage: `BlastN.runBlastNShort bcContext opt` Parameters: bcContext : `BcContext` opt : `BlastNShortParameters list`	run `blastn -task blastn-short` in the specified container context with the given commands bcContext : `BcContext` opt : `BlastNShortParameters list`
`BlastN.runBlastNShortAsync bcContext opt` Full Usage: `BlastN.runBlastNShortAsync bcContext opt` Parameters: bcContext : `BcContext` opt : `BlastNShortParameters list` Returns: `Async<unit>`	returns an asynchronous computation that will run `blastn -task blastn-short` in the specified container context with the given commands bcContext : `BcContext` opt : `BlastNShortParameters list` Returns: `Async<unit>`
`BlastN.runDCMegablastN bcContext opt` Full Usage: `BlastN.runDCMegablastN bcContext opt` Parameters: bcContext : `BcContext` opt : `DCMegablastParameters list`	run `blastn -task dc-megablast` in the specified container context with the given commands bcContext : `BcContext` opt : `DCMegablastParameters list`
`BlastN.runDCMegablastNAsync bcContext opt` Full Usage: `BlastN.runDCMegablastNAsync bcContext opt` Parameters: bcContext : `BcContext` opt : `DCMegablastParameters list` Returns: `Async<unit>`	returns an asynchronous computation that will run `blastn -task dc-megablast` in the specified container context with the given commands bcContext : `BcContext` opt : `DCMegablastParameters list` Returns: `Async<unit>`
`BlastN.runMegablast bcContext opt` Full Usage: `BlastN.runMegablast bcContext opt` Parameters: bcContext : `BcContext` opt : `MegablastParameters list`	run `blastn -task megablast` in the specified container context with the given commands bcContext : `BcContext` opt : `MegablastParameters list`
`BlastN.runMegablastAsync bcContext opt` Full Usage: `BlastN.runMegablastAsync bcContext opt` Parameters: bcContext : `BcContext` opt : `MegablastParameters list` Returns: `Async<unit>`	returns an asynchronous computation that will run `blastn -task megablast` in the specified container context with the given commands bcContext : `BcContext` opt : `MegablastParameters list` Returns: `Async<unit>`