Pairwise Fasta alignment against local file
Code sample below shows how to align sequences stored in a given FASTA formatted file against a local file using Fasta.
Imports System
Imports System.Collections
Imports Biolomics.BioCallback
Imports Biolomics.SharedClasses
Public Class MyNewClass
' This function is called when running this script
Shared Sub Main()
' Create an instance of class MyNewClass and call its functions
Dim c As New MyNewClass
c.FastaAlign()
End Sub
Public Sub FastaAlign()
' ********** Fasta align with local file ****************
Dim Options As New XBlastOptions
' for your information, default values are:
Options.GapCreationPenalty = 12
Options.GapExtensionPenalty = 2
Options.PenaltyMisMatch = -2
Options.RewardMatch = 1
Options.WordSize = 11
Options.MaxSequencesDisplayed = 100
Options.MaxTimeMinutesAllowed = 5
Options.SortingMode = BlastSortingModeEnum.Rating
' you can change these options for a fine tuning of the alignment
Options.MaxSequencesDisplayed = 5
' Alignment against a local reference fasta file
Dim QueryFastaFile As String = "D:\Temp\Sequences.fas" 'full path of Fasta formatted file to be aligned with a reference database available on disk
Dim ReferenceFastaFile As String = "D:\Temp\AllRefSequences.fas"
Dim ResultList As New Generic.List(Of XFastaResultFile)
' last parameter must be set only once, especially if the reference file is big
Run.FastaAlignWithLocalFile(ResultList, QueryFastaFile, ReferenceFastaFile, Options, BlastTypeEnum.Fastan, BlastRefFileFormatEnum.Dna)
' the names of the result files and the alignment results are stored in each XFastaResultFile object
End Sub
End Class