public static int PairwiseAlignSequences(
	ref string p_AlignmentResult,
	string p_SequenceOne,
	string p_SequenceTwo,
	bool p_SequenceOneIsdna = true,
	bool p_SequenceTwoIsdna = true,
	bool p_BlastAlgorithm = true,
	int p_GapCreationPenalty = 12,
	int p_GapExtentionPenalty = 2,
	int p_PenaltyMissmatch = -2,
	int p_RewardMatch = 1,
	int p_WordSize = 11,
	int p_MaxSequencesDisplayed = 100
)

Public Shared Function PairwiseAlignSequences ( 
	ByRef p_AlignmentResult As String,
	p_SequenceOne As String,
	p_SequenceTwo As String,
	Optional p_SequenceOneIsdna As Boolean = true,
	Optional p_SequenceTwoIsdna As Boolean = true,
	Optional p_BlastAlgorithm As Boolean = true,
	Optional p_GapCreationPenalty As Integer = 12,
	Optional p_GapExtentionPenalty As Integer = 2,
	Optional p_PenaltyMissmatch As Integer = -2,
	Optional p_RewardMatch As Integer = 1,
	Optional p_WordSize As Integer = 11,
	Optional p_MaxSequencesDisplayed As Integer = 100
) As Integer

Imports System
Imports BioloMICS.BioCallback
Imports BioloMICS.SharedClasses
Imports System.Collections

Public Class Program

    <STAThread()>
    Shared Sub Main()
        '    Create an instance of class Program and call its functions
        Dim c As New Program
        c.BlastAlign()
    End Sub

    Public Sub BlastAlign()
        '    Blast aligment
        Dim Results As String = ""
        Dim SequenceOne As String = "agtcatatgcttgtctcaaagattaagccatgcatagtctaagtttaagcaataaacagtgaaactgcgaatggctcattaaatcagtccatagtctatttgatggtaccttactacatggaaataactgtggtaattctagagctaatacatgctgaaaaatcccgacttctggaagggatgtatttattagatccaaaaccaacggccttcgggtctccttggtgaatcatgataactgctcgaatcgcatggccttgcgccggcgatgcttcattcgaatatctgccctatcaactttcgatggtaggatagaggcctaccatggtgatgacgggtaacggggaataagggttcgattccggagagagggcctgagaaacggccctcaggtctaaggacacgcagcaggcgcgcaaattatcccctggcaacactttgccgagatagtgacaataaataaca"
        Dim SequenceTwo As String = "agtcatatgcttgtctcaaagattaagccatgcatgtctaagtttaagcaataaacagcctgaaactgcgaatggctcattaaatcagtcatagtctatttgatggtaccttactacatggataactgtggtaatgtctagagctaatacatgctgaaaaatcccgacttctggaagggatgtatttattagatccaaaaccaacggccttcgggtctccttggtgaatcatgataactgctcgaatcgcatggccttgcgccggcgatgcttcattcgaatatctgccctatcaactttcgatggtaggatagaggcctaccatggtgatgacgggtaacggggaataagggttcgattccggagagagggcctgagaaacggccctcaggtctaaggacacgcagcaggcgcgcaaattatcccctggcaacactttgccgagatagtgacaataaataaca"

        '    the most simple call is this one:
        Run.PairwiseAlignSequences(Results, SequenceOne, SequenceTwo)
        Console.Write(Results)

        '    but you can specify more parameters for a fine tuning of the alignment
        Dim SequenceOneIsDNA As Boolean = True 'true for nucleotides, false for proteins
        Dim SequenceTwoIsDNA As Boolean = True 'true for nucleotides, false for proteins
        Dim UseBlastToAlign As Boolean = True 'true for BLAST, false for FASTA
        Dim GapCreationPenalty As Integer = 12 'must be between 2 and 100
        Dim GapExtentionPenalty As Integer = 2 'must be between 2 and 10
        Dim PenaltyMissmatch As Integer = -2 'must be between -5 and -2
        Dim RewardMatch As Integer = 1 'must be between 1 and 4
        Dim WordSize As Integer = 11  'must be between 7 and 20
        Dim MaximumSequencesDisplayed As Integer = 1 'should be one

        Run.PairwiseAlignSequences(Results, SequenceOne, SequenceTwo, SequenceOneIsDNA, SequenceTwoIsDNA, UseBlastToAlign, GapCreationPenalty, GapExtentionPenalty, PenaltyMissmatch, RewardMatch, WordSize, MaximumSequencesDisplayed)

        Console.Write("Second result:")
        Console.Write(Results)
    End Sub

End Class