XBlastHit Class |
Namespace: Biolomics.BioCallback
The XBlastHit type exposes the following members.
Name | Description | |
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Accession |
Gets the accession.
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BlastHitHspList |
Gets the blast hit HSP list.
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Def |
Gets the definition.
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Id |
Gets the Id.
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Len |
Gets the length.
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Num |
Gets the number.
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Name | Description | |
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BlastHitType |
Gets the BlastHitType .
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Direction |
Direction: string representation of the direction 'x/y' with:
x = '+' (Forward) or '-' (Backward) for the Query
y = '+' (Forward) or '-' (Backward) for the Subject
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Equals | Determines whether the specified object is equal to the current object. (Inherited from Object.) | |
Finalize | Allows an object to try to free resources and perform other cleanup operations before it is reclaimed by garbage collection. (Inherited from Object.) | |
GetHashCode | Serves as the default hash function. (Inherited from Object.) | |
GetType | Gets the Type of the current instance. (Inherited from Object.) | |
GlobalOverlap |
calculates the global overlap for all matching hits.
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GlobalProbability |
Returns the probability of the best hit segment pair
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GlobalScore |
Returns the bit_score of the best hit segment pair.
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GlobalSimilarity |
global similarity rate given by : (Total identity / Total length).
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GreatestHitHsp |
Returns the bit_score of the best hit segment pair.
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MemberwiseClone | Creates a shallow copy of the current Object. (Inherited from Object.) | |
ToString |
Returns a String that represents this instance.
(Overrides ObjectToString.) | |
TotalLen |
TotalLen: calculates the total length of the alignment segments
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Name | Description | |
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Equality |
Implements the operator =.
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Inequality |
Implements the operator <> operator.
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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.PairwiseAlignmentAgainstGenbank() End Sub Public Sub PairwiseAlignmentAgainstGenbank() ' ********** Align with Genbank ******** Dim QueryFastaFile As String = "Your_Fasta_File_Path\Sequences.fas" 'full path of Fasta formatted file to be aligned with a reference database available from Genbank Dim resultFastaFile As String = "Your_ResultFastaFile_Name.fas" 'full path of Fasta formatted file to be aligned with a reference database available from Genbank ' Genbank database. Possible options are: '"nr", "pat", "pdb", "month", "refseq_rna", "refseq_genomic", "est", "est_human", "est_mouse", "est_others", "gss", "htgs", "dbsts", "chromosome", "wgs", "env_nt" Dim MaxTimeMinutesAllowed As Integer = 2 ' maximum allowed time in minutes for a single query to be done. If longer, process will be canceled Dim StartTime As System.DateTime = System.DateTime.Now 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: Options.MaxSequencesDisplayed = 5 ' make a list for the results Dim Results As New Generic.List(Of Generic.List(Of XBlastHit)) ' query Genbank Dim ErrorCode As Integer = Run.BlastAlignWithGenbank(Results, resultFastaFile, QueryFastaFile, Options, GenBankDBNameEnum.nr) Dim ElapsedTicks As Long = System.DateTime.Now.Ticks - StartTime.Ticks Dim ElapsedSpan As New TimeSpan(ElapsedTicks) If ErrorCode = 0 Then Console.Write("Job done in " & CStr(ElapsedSpan.TotalSeconds) & " seconds") Console.Write("Results can then be viewed using the 'Open previous pairwise alignments (NxM)' menu under the 'Sequences' menu of the main BioloMICS Editor window") ' but you can also use the XBlastHit properties directly. Else For Each Err As String In Run.GetLastErrorMessage() Console.Write(Err) Next End If End Sub End Class