Text search with long "artificial" word

Dear All,
I have created one table which contains a clob column. The column have a content like 'atgctctgc.....atgc' (around 10M per row) as one big "word". I'd like to find the rows which contains the pattern 'atgctggcctttcact' (around 20~30 characters) in clob column. I used dbms_lob.instr and it does the work but still not fast enough. I don't know if it's possible to use the ctxsys.context index to solve the problem.
BTW, i have tried the default setting and it doesn't work. I use the following syntax:
select * from t where contains(l_clob, 'atgccacagaagaga') >0
It throws me "no data found" which i can find hits using dbms_lob.inst.
I am confused how i can solve the problem.
Regards,
lik

Hi,
I think this is a biological data sequence, am I correct? I think better to search patterns is to have a look at Regular_expressions or BLAST. Here is a presentation about both techniques: [url http://www.oracle.com/technology/industries/life_sciences/presentations/lsday903_6_2_Myriad_Sequence.ppt]Biological data search. Another one is this: [url http://www.oracle.com/technology/industries/life_sciences/pdf/twp_ls_blast_10gr1_0904.pdf]Sequence Matching and Alignment in Oracle
If you want to go on with text, you must use wildcards to find it:
select * from t where contains(l_clob, '%atgccacagaagaga%') >0 The problem is that this is not the best kind of search for a text index (both sides a wildcard). This can be sped up, but I don't think it will help you because that's intended for shorter terms/words.
Hope that the above can help you
Herald ten Dam
http://htendam.wordpress.com

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    Fanny Liu
    TechNet Community Support

  • How can I search for partial matching words in various columns without needing to provide search text?

    I have a list of names in three columns - B2:B425, D2:406, & E2:30 where they were input by different people, so the names are worded differently. For example, I can have the name "Handler, Jones, & Wright" and someone else has the name
    listed as "Handler Corp." What I need is to find a formula or VBA macro code that can search through my list and notice the possible duplicates and highlight them. Since they are all different names, I cannot give it a unique "text" to
    search.
    I found a code posted in this forum from some time ago (for two columns) but it highlighted all these names that had no partial words in common. Perhaps you can look over the code below and modify it for me or provide me with another one? Please let me know
    if you need any further information to guide me. 
    Sub HighlightDups()
        Dim rg1 As Range, rg2 As Range, c As Range, d As Range
        Dim sTemp As String, sTempWords() As String, sTempDWords() As String
        Dim re As Object, mc As Object
        Dim i As Long, j As Long
        Dim sFirstAddress As String
    Set rg1 = Range("B2", Cells(Rows.Columns.Count, "B").End(xlUp))
    Set rg2 = Range("D2", Cells(Rows.Columns.Count, "D").End(xlUp))
    Set re = CreateObject("vbscript.regexp")
        re.Global = True
        re.ignorecase = True
    With Range(rg1, rg2)
        .Font.Color = vbBlack
        .Font.Bold = False
        .Interior.Color = xlNone
        .FormatConditions.Delete
    End With
    For Each c In rg1
      re.Pattern = "\b\w+\b"
      If re.test(c.Text) = True Then
        Set mc = re.Execute(c.Text)
            ReDim sTempWords(0 To mc.Count - 1)
            For i = 0 To UBound(sTempWords)
                sTempWords(i) = mc(i)
            Next i
        For i = 0 To UBound(sTempWords)
            Set d = rg2.Find(What:=sTempWords(i), _
                             LookIn:=xlValues, _
                             LookAt:=xlPart, _
                             MatchCase:=False)
            If Not d Is Nothing Then
                re.Pattern = "\b" & sTempWords(i) & "\b"
                sFirstAddress = d.Address
                Do
                        If re.test(d.Text) Then
                    With c
                        .Font.Color = vbWhite
                        .Font.Bold = True
                        .Interior.Color = vbBlue
                    End With
                    With d
                        .Font.Color = vbWhite
                        .Font.Bold = True
                        .Interior.Color = vbBlue
                    End With
                        End If
                    Set d = rg2.FindNext(after:=d)
                    Loop While Not d Is Nothing And d.Address <> sFirstAddress
            End If
        Next i
      End If
    Next c
    Set re = Nothing
    End Sub
     

    Programming/Code related questions should really be posed in one of the following forums
    Excel for Developers
    http://social.msdn.microsoft.com/Forums/en-US/exceldev
    Microsoft Office Programming
    http://answers.microsoft.com/en-us/office/forum/customize?page=1&tab=all&tm=1361680524815
    Tony Chen
    TechNet Community Support

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