I've written an excel function aim to change a RNA sequence to its
reverse complement (e.g. from "ACGUUGUA" to "UACAACGU") as:

Function ReverseComplement(Rcell As Range, Optional IsText As Boolean)

Dim i As Integer
Dim strReverseSeq As String
Dim strSenseSeq As String

strSenseSeq = Trim(Rcell)

For i = 1 To Len(strSenseSeq)
strReverseSeq = Mid(strSenseSeq, i, 1) & _ strReverseSeq
Next i

If IsText = False Then
ReverseComplement = CLng(strReverseSeq)
Else
ReverseComplement = strReverseSeq
End If

strSeqA1 = Replace(strReverseSeq, "A", "1")
strSeqC2 = Replace(strSeqA1, "C", "2")
strSeqG3 = Replace(strSeqC2, "G", "3")
strSeqT4 = Replace(strSeqG3, "U", "4")
strSeq1T = Replace(strSeqT4, "1", "U")
strSeq2G = Replace(strSeq1T, "2", "G")
strSeq3C = Replace(strSeq2G, "3", "C")
strSeq4A = Replace(strSeq3C, "4", "A")

End Function

The first half works fine, which reverse the sequence, but the second
part doesn't work, which cannot make the comoplements Please help for
debug. Much thanks.

*** Sent via Developersdex http://www.developersdex.com ***
Don't just participate in USENET...get rewarded for it!

As an example
Assume you had a reversed string like AAA

your code would convert it like this

AAA = 111 = UUU

If that is what you want, then Ok. If the problem is you would want 111 as
a result, then I think you need to go to an intermediate stage (two step
process)

AAA = MMM = 111

Where the middle stage would use unique identifiers so you wouldn't convert
any value after it was converted to a final value.

A to M, M to 1
C to N, N to 2
G to O, O to 3
U to P, P to 4
1 to Q, Q to U
2 to R, R to G
3 to S, S to C
4 to T, T to A

--
Regards,
Tom Ogilvy



"M H" wrote in message
...

I've written an excel function aim to change a RNA sequence to its
reverse complement (e.g. from "ACGUUGUA" to "UACAACGU") as:

Function ReverseComplement(Rcell As Range, Optional IsText As Boolean)

Dim i As Integer
Dim strReverseSeq As String
Dim strSenseSeq As String

strSenseSeq = Trim(Rcell)

For i = 1 To Len(strSenseSeq)
strReverseSeq = Mid(strSenseSeq, i, 1) & _ strReverseSeq
Next i

If IsText = False Then
ReverseComplement = CLng(strReverseSeq)
Else
ReverseComplement = strReverseSeq
End If

strSeqA1 = Replace(strReverseSeq, "A", "1")
strSeqC2 = Replace(strSeqA1, "C", "2")
strSeqG3 = Replace(strSeqC2, "G", "3")
strSeqT4 = Replace(strSeqG3, "U", "4")
strSeq1T = Replace(strSeqT4, "1", "U")
strSeq2G = Replace(strSeq1T, "2", "G")
strSeq3C = Replace(strSeq2G, "3", "C")
strSeq4A = Replace(strSeq3C, "4", "A")

End Function

The first half works fine, which reverse the sequence, but the second
part doesn't work, which cannot make the comoplements Please help for
debug. Much thanks.

*** Sent via Developersdex http://www.developersdex.com ***
Don't just participate in USENET...get rewarded for it!

Perhaps

Public Function ReverseComplement(sInput As String)
Dim sTemp As String
sTemp = UCase(Replace(Replace(Replace(Replace( _
sInput, "A", "u"), "C", "g"), "G", "c"), "U", "a"))
ReverseComplement = sTemp
End Function



In article ,
M H wrote:

I've written an excel function aim to change a RNA sequence to its
reverse complement (e.g. from "ACGUUGUA" to "UACAACGU") as:

Function ReverseComplement(Rcell As Range, Optional IsText As Boolean)

Dim i As Integer
Dim strReverseSeq As String
Dim strSenseSeq As String

strSenseSeq = Trim(Rcell)

For i = 1 To Len(strSenseSeq)
strReverseSeq = Mid(strSenseSeq, i, 1) & _ strReverseSeq
Next i

If IsText = False Then
ReverseComplement = CLng(strReverseSeq)
Else
ReverseComplement = strReverseSeq
End If

strSeqA1 = Replace(strReverseSeq, "A", "1")
strSeqC2 = Replace(strSeqA1, "C", "2")
strSeqG3 = Replace(strSeqC2, "G", "3")
strSeqT4 = Replace(strSeqG3, "U", "4")
strSeq1T = Replace(strSeqT4, "1", "U")
strSeq2G = Replace(strSeq1T, "2", "G")
strSeq3C = Replace(strSeq2G, "3", "C")
strSeq4A = Replace(strSeq3C, "4", "A")

End Function

The first half works fine, which reverse the sequence, but the second
part doesn't work, which cannot make the comoplements Please help for
debug. Much thanks.

*** Sent via Developersdex http://www.developersdex.com ***
Don't just participate in USENET...get rewarded for it!

And I'm not sure what you were after with the IsText, but if you want
ACGU to return 4321:

Public Function ReverseComplement(sInput As String, _
Optional bText As Boolean = True) As String
Dim sTemp As Variant
If bText Then
sTemp = UCase(Replace(Replace(Replace(Replace( _
sInput, "A", "u"), "C", "g"), "G", "c"), "U", "a"))
Else
sTemp = Replace(Replace(Replace(Replace( _
sInput, "A", "4"), "C", "3"), "G", "2"), "U", "1")
End If
ReverseComplement = sTemp
End Function




In article ,
JE McGimpsey wrote:

Perhaps

Public Function ReverseComplement(sInput As String)
Dim sTemp As String
sTemp = UCase(Replace(Replace(Replace(Replace( _
sInput, "A", "u"), "C", "g"), "G", "c"), "U", "a"))
ReverseComplement = sTemp
End Function

Nice one, JE! I think he also wants the characters in reverse order, so
perhaps this slight modification will take care of that:

Public Function ReverseComplement(sInput As String)
Dim sTemp As String
sTemp = UCase(Replace(Replace(Replace(Replace( _
sInput, "A", "u"), "C", "g"), "G", "c"), "U", "a"))
ReverseComplement = StrReverse(sTemp)
End Function

On Mon, 17 Jan 2005 11:43:12 -0700, JE McGimpsey wrote:

Perhaps

Public Function ReverseComplement(sInput As String)
Dim sTemp As String
sTemp = UCase(Replace(Replace(Replace(Replace( _
sInput, "A", "u"), "C", "g"), "G", "c"), "U", "a"))
ReverseComplement = sTemp
End Function



In article ,
M H wrote:

I've written an excel function aim to change a RNA sequence to its
reverse complement (e.g. from "ACGUUGUA" to "UACAACGU") as:

Function ReverseComplement(Rcell As Range, Optional IsText As Boolean)

Dim i As Integer
Dim strReverseSeq As String
Dim strSenseSeq As String

strSenseSeq = Trim(Rcell)

For i = 1 To Len(strSenseSeq)
strReverseSeq = Mid(strSenseSeq, i, 1) & _ strReverseSeq
Next i

If IsText = False Then
ReverseComplement = CLng(strReverseSeq)
Else
ReverseComplement = strReverseSeq
End If

strSeqA1 = Replace(strReverseSeq, "A", "1")
strSeqC2 = Replace(strSeqA1, "C", "2")
strSeqG3 = Replace(strSeqC2, "G", "3")
strSeqT4 = Replace(strSeqG3, "U", "4")
strSeq1T = Replace(strSeqT4, "1", "U")
strSeq2G = Replace(strSeq1T, "2", "G")
strSeq3C = Replace(strSeq2G, "3", "C")
strSeq4A = Replace(strSeq3C, "4", "A")

End Function

The first half works fine, which reverse the sequence, but the second
part doesn't work, which cannot make the comoplements Please help for
debug. Much thanks.

*** Sent via Developersdex http://www.developersdex.com ***
Don't just participate in USENET...get rewarded for it!

Thanks, Myrna - I missed that!

In article ,
Myrna Larson wrote:

I think he also wants the characters in reverse order, so
perhaps this slight modification will take care of that:

After looking more closely, (you didn't say what you error/problem was
exactly and I don't know anything about RNA), I see you have just failed to
assign the result to the function name.

Function ReverseComplement(Rcell As Range)

Dim i As Integer
Dim strReverseSeq As String
Dim strSenseSeq As String

strSenseSeq = Trim(Rcell)

For i = 1 To Len(strSenseSeq)
strReverseSeq = Mid(strSenseSeq, i, 1) & _
strReverseSeq
Next i


strSeqA1 = Replace(strReverseSeq, "A", "1")
strSeqC2 = Replace(strSeqA1, "C", "2")
strSeqG3 = Replace(strSeqC2, "G", "3")
strSeqT4 = Replace(strSeqG3, "U", "4")
strSeq1T = Replace(strSeqT4, "1", "U")
strSeq2G = Replace(strSeq1T, "2", "G")
strSeq3C = Replace(strSeq2G, "3", "C")
strSeq4A = Replace(strSeq3C, "4", "A")
ReverseComplement = strSeq4A
End Function


I don't see any reason for the istext argument as there is no reason to
convert to clng.

--
Regards,
Tom Ogilvy

"Tom Ogilvy" wrote in message
...
As an example
Assume you had a reversed string like AAA

your code would convert it like this

AAA = 111 = UUU

If that is what you want, then Ok. If the problem is you would want 111
as
a result, then I think you need to go to an intermediate stage (two step
process)

AAA = MMM = 111

Where the middle stage would use unique identifiers so you wouldn't
convert
any value after it was converted to a final value.

A to M, M to 1
C to N, N to 2
G to O, O to 3
U to P, P to 4
1 to Q, Q to U
2 to R, R to G
3 to S, S to C
4 to T, T to A

--
Regards,
Tom Ogilvy



"M H" wrote in message
...

I've written an excel function aim to change a RNA sequence to its
reverse complement (e.g. from "ACGUUGUA" to "UACAACGU") as:

Function ReverseComplement(Rcell As Range, Optional IsText As Boolean)

Dim i As Integer
Dim strReverseSeq As String
Dim strSenseSeq As String

strSenseSeq = Trim(Rcell)

For i = 1 To Len(strSenseSeq)
strReverseSeq = Mid(strSenseSeq, i, 1) & _ strReverseSeq
Next i

If IsText = False Then
ReverseComplement = CLng(strReverseSeq)
Else
ReverseComplement = strReverseSeq
End If

strSeqA1 = Replace(strReverseSeq, "A", "1")
strSeqC2 = Replace(strSeqA1, "C", "2")
strSeqG3 = Replace(strSeqC2, "G", "3")
strSeqT4 = Replace(strSeqG3, "U", "4")
strSeq1T = Replace(strSeqT4, "1", "U")
strSeq2G = Replace(strSeq1T, "2", "G")
strSeq3C = Replace(strSeq2G, "3", "C")
strSeq4A = Replace(strSeq3C, "4", "A")

End Function

The first half works fine, which reverse the sequence, but the second
part doesn't work, which cannot make the comoplements Please help for
debug. Much thanks.

*** Sent via Developersdex http://www.developersdex.com ***
Don't just participate in USENET...get rewarded for it!

If the objective is to pack everything together, why stop there

Public Function ReverseComplement(sInput As String)
ReverseComplement = _
StrReverse(UCase(Replace(Replace(Replace(Replace( _
sInput, "A", "u"), "C", "g"), "G", "c"), "U", "a")))
End Function

---
Regards,
Tom Ogilvy

"Myrna Larson" wrote in message
...
Nice one, JE! I think he also wants the characters in reverse order, so
perhaps this slight modification will take care of that:

Public Function ReverseComplement(sInput As String)
Dim sTemp As String
sTemp = UCase(Replace(Replace(Replace(Replace( _
sInput, "A", "u"), "C", "g"), "G", "c"), "U", "a"))
ReverseComplement = StrReverse(sTemp)
End Function

On Mon, 17 Jan 2005 11:43:12 -0700, JE McGimpsey
wrote:

Perhaps

Public Function ReverseComplement(sInput As String)
Dim sTemp As String
sTemp = UCase(Replace(Replace(Replace(Replace( _
sInput, "A", "u"), "C", "g"), "G", "c"), "U", "a"))
ReverseComplement = sTemp
End Function



In article ,
M H wrote:

I've written an excel function aim to change a RNA sequence to its
reverse complement (e.g. from "ACGUUGUA" to "UACAACGU") as:

Function ReverseComplement(Rcell As Range, Optional IsText As Boolean)

Dim i As Integer
Dim strReverseSeq As String
Dim strSenseSeq As String

strSenseSeq = Trim(Rcell)

For i = 1 To Len(strSenseSeq)
strReverseSeq = Mid(strSenseSeq, i, 1) & _ strReverseSeq
Next i

If IsText = False Then
ReverseComplement = CLng(strReverseSeq)
Else
ReverseComplement = strReverseSeq
End If

strSeqA1 = Replace(strReverseSeq, "A", "1")
strSeqC2 = Replace(strSeqA1, "C", "2")
strSeqG3 = Replace(strSeqC2, "G", "3")
strSeqT4 = Replace(strSeqG3, "U", "4")
strSeq1T = Replace(strSeqT4, "1", "U")
strSeq2G = Replace(strSeq1T, "2", "G")
strSeq3C = Replace(strSeq2G, "3", "C")
strSeq4A = Replace(strSeq3C, "4", "A")

End Function

The first half works fine, which reverse the sequence, but the second
part doesn't work, which cannot make the comoplements Please help for
debug. Much thanks.

*** Sent via Developersdex http://www.developersdex.com ***
Don't just participate in USENET...get rewarded for it!

The objective (in my case) was to avoid a series of explicit transition
steps (e.g, A-1-U, C-2-G,...), reducing 8 Replace's to 4 + a UCase().

Whether StrReverse is applied to an named or unnamed temporary variable
is probably irrelevant.

For clarity, if nothing else, I generally use temporary variables in the
function, making an explicit assignment to the function's returned
variable at the very end.

In article ,
"Tom Ogilvy" wrote:

If the objective is to pack everything together, why stop there

Public Function ReverseComplement(sInput As String)
ReverseComplement = _
StrReverse(UCase(Replace(Replace(Replace(Replace( _
sInput, "A", "u"), "C", "g"), "G", "c"), "U", "a")))
End Function

I guess my objective in this case is more to show the OP what steps are to be
taken. To demonstrate as a learning tool, I would have done the replacements
as 4 steps (as the OP had done originally), a 5th line to to the UCase, a 6th
for the StrReverse, and a 7th to assign to the function output. I don't know
whether in the real world that is slower or faster than combining everything
into one statement.

On Mon, 17 Jan 2005 14:37:08 -0500, "Tom Ogilvy" wrote:

If the objective is to pack everything together, why stop there

Public Function ReverseComplement(sInput As String)
ReverseComplement = _
StrReverse(UCase(Replace(Replace(Replace(Replace( _
sInput, "A", "u"), "C", "g"), "G", "c"), "U", "a")))
End Function

---
Regards,
Tom Ogilvy

"Myrna Larson" wrote in message
.. .
Nice one, JE! I think he also wants the characters in reverse order, so
perhaps this slight modification will take care of that:

Public Function ReverseComplement(sInput As String)
Dim sTemp As String
sTemp = UCase(Replace(Replace(Replace(Replace( _
sInput, "A", "u"), "C", "g"), "G", "c"), "U", "a"))
ReverseComplement = StrReverse(sTemp)
End Function

On Mon, 17 Jan 2005 11:43:12 -0700, JE McGimpsey
wrote:

Perhaps

Public Function ReverseComplement(sInput As String)
Dim sTemp As String
sTemp = UCase(Replace(Replace(Replace(Replace( _
sInput, "A", "u"), "C", "g"), "G", "c"), "U", "a"))
ReverseComplement = sTemp
End Function



In article ,
M H wrote:

I've written an excel function aim to change a RNA sequence to its
reverse complement (e.g. from "ACGUUGUA" to "UACAACGU") as:

Function ReverseComplement(Rcell As Range, Optional IsText As Boolean)

Dim i As Integer
Dim strReverseSeq As String
Dim strSenseSeq As String

strSenseSeq = Trim(Rcell)

For i = 1 To Len(strSenseSeq)
strReverseSeq = Mid(strSenseSeq, i, 1) & _ strReverseSeq
Next i

If IsText = False Then
ReverseComplement = CLng(strReverseSeq)
Else
ReverseComplement = strReverseSeq
End If

strSeqA1 = Replace(strReverseSeq, "A", "1")
strSeqC2 = Replace(strSeqA1, "C", "2")
strSeqG3 = Replace(strSeqC2, "G", "3")
strSeqT4 = Replace(strSeqG3, "U", "4")
strSeq1T = Replace(strSeqT4, "1", "U")
strSeq2G = Replace(strSeq1T, "2", "G")
strSeq3C = Replace(strSeq2G, "3", "C")
strSeq4A = Replace(strSeq3C, "4", "A")

End Function

The first half works fine, which reverse the sequence, but the second
part doesn't work, which cannot make the comoplements Please help for
debug. Much thanks.

*** Sent via Developersdex http://www.developersdex.com ***
Don't just participate in USENET...get rewarded for it!

I was impressed not by JE's use of a single statement, but by replacing with a
lower case letter instead of a number, symbol or different letter altogether.
The first approach requires 4 replacements plus the UCase$; the latter
requires 8 replacements.

On Mon, 17 Jan 2005 14:37:08 -0500, "Tom Ogilvy" wrote:

If the objective is to pack everything together, why stop there

Public Function ReverseComplement(sInput As String)
ReverseComplement = _
StrReverse(UCase(Replace(Replace(Replace(Replace( _
sInput, "A", "u"), "C", "g"), "G", "c"), "U", "a")))
End Function

---
Regards,
Tom Ogilvy

"Myrna Larson" wrote in message
.. .
Nice one, JE! I think he also wants the characters in reverse order, so
perhaps this slight modification will take care of that:

Public Function ReverseComplement(sInput As String)
Dim sTemp As String
sTemp = UCase(Replace(Replace(Replace(Replace( _
sInput, "A", "u"), "C", "g"), "G", "c"), "U", "a"))
ReverseComplement = StrReverse(sTemp)
End Function

On Mon, 17 Jan 2005 11:43:12 -0700, JE McGimpsey
wrote:

Perhaps

Public Function ReverseComplement(sInput As String)
Dim sTemp As String
sTemp = UCase(Replace(Replace(Replace(Replace( _
sInput, "A", "u"), "C", "g"), "G", "c"), "U", "a"))
ReverseComplement = sTemp
End Function



In article ,
M H wrote:

I've written an excel function aim to change a RNA sequence to its
reverse complement (e.g. from "ACGUUGUA" to "UACAACGU") as:

Function ReverseComplement(Rcell As Range, Optional IsText As Boolean)

Dim i As Integer
Dim strReverseSeq As String
Dim strSenseSeq As String

strSenseSeq = Trim(Rcell)

For i = 1 To Len(strSenseSeq)
strReverseSeq = Mid(strSenseSeq, i, 1) & _ strReverseSeq
Next i

If IsText = False Then
ReverseComplement = CLng(strReverseSeq)
Else
ReverseComplement = strReverseSeq
End If

strSeqA1 = Replace(strReverseSeq, "A", "1")
strSeqC2 = Replace(strSeqA1, "C", "2")
strSeqG3 = Replace(strSeqC2, "G", "3")
strSeqT4 = Replace(strSeqG3, "U", "4")
strSeq1T = Replace(strSeqT4, "1", "U")
strSeq2G = Replace(strSeq1T, "2", "G")
strSeq3C = Replace(strSeq2G, "3", "C")
strSeq4A = Replace(strSeq3C, "4", "A")

End Function

The first half works fine, which reverse the sequence, but the second
part doesn't work, which cannot make the comoplements Please help for
debug. Much thanks.

*** Sent via Developersdex http://www.developersdex.com ***
Don't just participate in USENET...get rewarded for it!

Hi,
sorry did not find the original posting so I answer this one.
I see how you reverse the strand .
I do not understand how you want to complement the strand.
So I can not comment your solution.
But have a solution for the problem if you want.
Feel free to adapt it to your needs.

'This function converts a DNA string to its
'reverse complement
'Gys de Jongh 16-jun-1999
Function Rev(Forw As String) As String
Dim ForwA(1 To 100) As String * 1
Dim RevA(1 To 100) As String * 1
N = Len(Forw)
If N 100 Then
Rev = "Input too long (max 100)"
Exit Function
End If
For I = 1 To N
ForwA(I) = Mid(Forw, I, 1)
Next I
For I = 1 To N
Select Case ForwA(N - I + 1)
Case "A"
RevA(I) = "T"
Case "a"
RevA(I) = "t"
'From A to T
Case "C"
RevA(I) = "G"
Case "c"
RevA(I) = "g"
'From C to G
Case "G"
RevA(I) = "C"
Case "g"
RevA(I) = "c"
'From G to C
Case "T"
RevA(I) = "A"
Case "t"
RevA(I) = "a"
'From T to A
Case Else
RevA(I) = "N"
'Rest is N
End Select
Next I
For I = 1 To N
Rev = Rev & RevA(I)
Next I
End Function

Short explanation for Tom :
DNA contains the information for cells
It is a double helix with 2 strings , molecules
The two strings contain the same information
They are redundant , one can be used to construct the other
In each string A only pairs with T and C only with G
But :
the Sense strand reads from left to right and
the anti Sense strand from right to left
so :

ACGTCCCTGAAATT <====Sense strand
TGCAGGGACTTTAA <====anti Sense strand

Finding the reverse complement means finding the other if one is known

hth
Gys




"Tom Ogilvy" wrote in message
...
As an example
Assume you had a reversed string like AAA

your code would convert it like this

AAA = 111 = UUU

If that is what you want, then Ok. If the problem is you would want 111 as
a result, then I think you need to go to an intermediate stage (two step
process)

AAA = MMM = 111

Where the middle stage would use unique identifiers so you wouldn't convert
any value after it was converted to a final value.

A to M, M to 1
C to N, N to 2
G to O, O to 3
U to P, P to 4
1 to Q, Q to U
2 to R, R to G
3 to S, S to C
4 to T, T to A

--
Regards,
Tom Ogilvy



"M H" wrote in message
...

I've written an excel function aim to change a RNA sequence to its
reverse complement (e.g. from "ACGUUGUA" to "UACAACGU") as:

Function ReverseComplement(Rcell As Range, Optional IsText As Boolean)

Dim i As Integer
Dim strReverseSeq As String
Dim strSenseSeq As String

strSenseSeq = Trim(Rcell)

For i = 1 To Len(strSenseSeq)
strReverseSeq = Mid(strSenseSeq, i, 1) & _ strReverseSeq
Next i

If IsText = False Then
ReverseComplement = CLng(strReverseSeq)
Else
ReverseComplement = strReverseSeq
End If

strSeqA1 = Replace(strReverseSeq, "A", "1")

here strSeqA1 etc are just a not declared variables which don't seem to reach
the output of the function ????

strSeqC2 = Replace(strSeqA1, "C", "2")
strSeqG3 = Replace(strSeqC2, "G", "3")
strSeqT4 = Replace(strSeqG3, "U", "4")
strSeq1T = Replace(strSeqT4, "1", "U")
strSeq2G = Replace(strSeq1T, "2", "G")
strSeq3C = Replace(strSeq2G, "3", "C")
strSeq4A = Replace(strSeq3C, "4", "A")

End Function

The first half works fine, which reverse the sequence, but the second
part doesn't work, which cannot make the comoplements Please help for
debug. Much thanks.

*** Sent via Developersdex http://www.developersdex.com ***
Don't just participate in USENET...get rewarded for it!

Hi,
sorry did not find the original posting so I answer this one.
I see how you reverse the strand .
I do not understand how you want to complement the strand.
So I can not comment your solution.
But have a solution for the problem if you want.
Feel free to adapt it to your needs.

'This function converts a DNA string to its
'reverse complement
'Gys de Jongh 16-jun-1999
Function Rev(Forw As String) As String
Dim ForwA(1 To 100) As String * 1
Dim RevA(1 To 100) As String * 1
N = Len(Forw)
If N 100 Then
Rev = "Input too long (max 100)"
Exit Function
End If
For I = 1 To N
ForwA(I) = Mid(Forw, I, 1)
Next I
For I = 1 To N
Select Case ForwA(N - I + 1)
Case "A"
RevA(I) = "T"
Case "a"
RevA(I) = "t"
'From A to T
Case "C"
RevA(I) = "G"
Case "c"
RevA(I) = "g"
'From C to G
Case "G"
RevA(I) = "C"
Case "g"
RevA(I) = "c"
'From G to C
Case "T"
RevA(I) = "A"
Case "t"
RevA(I) = "a"
'From T to A
Case Else
RevA(I) = "N"
'Rest is N
End Select
Next I
For I = 1 To N
Rev = Rev & RevA(I)
Next I
End Function

Short explanation for Tom :
DNA contains the information for cells
It is a double helix with 2 strings , molecules
The two strings contain the same information
They are redundant , one can be used to construct the other
In each string A only pairs with T and C only with G
But :
the Sense strand reads from left to right and
the anti Sense strand from right to left
so :

ACGTCCCTGAAATT <====Sense strand
TGCAGGGACTTTAA <====anti Sense strand

Finding the reverse complement means finding the other if one is known

hth
Gys





"Tom Ogilvy" wrote in message
...
As an example
Assume you had a reversed string like AAA

your code would convert it like this

AAA = 111 = UUU

If that is what you want, then Ok. If the problem is you would want 111 as
a result, then I think you need to go to an intermediate stage (two step
process)

AAA = MMM = 111

Where the middle stage would use unique identifiers so you wouldn't convert
any value after it was converted to a final value.

A to M, M to 1
C to N, N to 2
G to O, O to 3
U to P, P to 4
1 to Q, Q to U
2 to R, R to G
3 to S, S to C
4 to T, T to A

--
Regards,
Tom Ogilvy



"M H" wrote in message
...

I've written an excel function aim to change a RNA sequence to its
reverse complement (e.g. from "ACGUUGUA" to "UACAACGU") as:

Function ReverseComplement(Rcell As Range, Optional IsText As Boolean)

Dim i As Integer
Dim strReverseSeq As String
Dim strSenseSeq As String

strSenseSeq = Trim(Rcell)

For i = 1 To Len(strSenseSeq)
strReverseSeq = Mid(strSenseSeq, i, 1) & _ strReverseSeq
Next i

If IsText = False Then
ReverseComplement = CLng(strReverseSeq)
Else
ReverseComplement = strReverseSeq
End If

strSeqA1 = Replace(strReverseSeq, "A", "1")
strSeqC2 = Replace(strSeqA1, "C", "2")
strSeqG3 = Replace(strSeqC2, "G", "3")
strSeqT4 = Replace(strSeqG3, "U", "4")
strSeq1T = Replace(strSeqT4, "1", "U")
strSeq2G = Replace(strSeq1T, "2", "G")
strSeq3C = Replace(strSeq2G, "3", "C")
strSeq4A = Replace(strSeq3C, "4", "A")

End Function

The first half works fine, which reverse the sequence, but the second
part doesn't work, which cannot make the comoplements Please help for
debug. Much thanks.

*** Sent via Developersdex http://www.developersdex.com ***
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I believe By Complement, he means interchange A and T and C and G, as you (and
he) are doing.

But why do you not want to use Replace, StrReverse and UCase$? The code is
much shorter -- it can be reduced to just 7 lines.

On Mon, 17 Jan 2005 23:56:04 +0100, "GysdeJongh" wrote:

Hi,
sorry did not find the original posting so I answer this one.
I see how you reverse the strand .
I do not understand how you want to complement the strand.
So I can not comment your solution.
But have a solution for the problem if you want.
Feel free to adapt it to your needs.

'This function converts a DNA string to its
'reverse complement
'Gys de Jongh 16-jun-1999
Function Rev(Forw As String) As String
Dim ForwA(1 To 100) As String * 1
Dim RevA(1 To 100) As String * 1
N = Len(Forw)
If N 100 Then
Rev = "Input too long (max 100)"
Exit Function
End If
For I = 1 To N
ForwA(I) = Mid(Forw, I, 1)
Next I
For I = 1 To N
Select Case ForwA(N - I + 1)
Case "A"
RevA(I) = "T"
Case "a"
RevA(I) = "t"
'From A to T
Case "C"
RevA(I) = "G"
Case "c"
RevA(I) = "g"
'From C to G
Case "G"
RevA(I) = "C"
Case "g"
RevA(I) = "c"
'From G to C
Case "T"
RevA(I) = "A"
Case "t"
RevA(I) = "a"
'From T to A
Case Else
RevA(I) = "N"
'Rest is N
End Select
Next I
For I = 1 To N
Rev = Rev & RevA(I)
Next I
End Function

Short explanation for Tom :
DNA contains the information for cells
It is a double helix with 2 strings , molecules
The two strings contain the same information
They are redundant , one can be used to construct the other
In each string A only pairs with T and C only with G
But :
the Sense strand reads from left to right and
the anti Sense strand from right to left
so :

ACGTCCCTGAAATT <====Sense strand
TGCAGGGACTTTAA <====anti Sense strand

Finding the reverse complement means finding the other if one is known

hth
Gys





"Tom Ogilvy" wrote in message
...
As an example
Assume you had a reversed string like AAA

your code would convert it like this

AAA = 111 = UUU

If that is what you want, then Ok. If the problem is you would want 111 as
a result, then I think you need to go to an intermediate stage (two step
process)

AAA = MMM = 111

Where the middle stage would use unique identifiers so you wouldn't convert
any value after it was converted to a final value.

A to M, M to 1
C to N, N to 2
G to O, O to 3
U to P, P to 4
1 to Q, Q to U
2 to R, R to G
3 to S, S to C
4 to T, T to A

--
Regards,
Tom Ogilvy



"M H" wrote in message
...

I've written an excel function aim to change a RNA sequence to its
reverse complement (e.g. from "ACGUUGUA" to "UACAACGU") as:

Function ReverseComplement(Rcell As Range, Optional IsText As Boolean)

Dim i As Integer
Dim strReverseSeq As String
Dim strSenseSeq As String

strSenseSeq = Trim(Rcell)

For i = 1 To Len(strSenseSeq)
strReverseSeq = Mid(strSenseSeq, i, 1) & _ strReverseSeq
Next i

If IsText = False Then
ReverseComplement = CLng(strReverseSeq)
Else
ReverseComplement = strReverseSeq
End If

strSeqA1 = Replace(strReverseSeq, "A", "1")
strSeqC2 = Replace(strSeqA1, "C", "2")
strSeqG3 = Replace(strSeqC2, "G", "3")
strSeqT4 = Replace(strSeqG3, "U", "4")
strSeq1T = Replace(strSeqT4, "1", "U")
strSeq2G = Replace(strSeq1T, "2", "G")
strSeq3C = Replace(strSeq2G, "3", "C")
strSeq4A = Replace(strSeq3C, "4", "A")

End Function

The first half works fine, which reverse the sequence, but the second
part doesn't work, which cannot make the comoplements Please help for
debug. Much thanks.

*** Sent via Developersdex http://www.developersdex.com ***
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Bad choice of words.

--
Regards,
Tom Ogilvy

"Myrna Larson" wrote in message
...
I was impressed not by JE's use of a single statement, but by replacing
with a
lower case letter instead of a number, symbol or different letter
altogether.
The first approach requires 4 replacements plus the UCase$; the latter
requires 8 replacements.

On Mon, 17 Jan 2005 14:37:08 -0500, "Tom Ogilvy" wrote:

If the objective is to pack everything together, why stop there

Public Function ReverseComplement(sInput As String)
ReverseComplement = _
StrReverse(UCase(Replace(Replace(Replace(Replace( _
sInput, "A", "u"), "C", "g"), "G", "c"), "U", "a")))
End Function

---
Regards,
Tom Ogilvy

"Myrna Larson" wrote in message
.. .
Nice one, JE! I think he also wants the characters in reverse order, so
perhaps this slight modification will take care of that:

Public Function ReverseComplement(sInput As String)
Dim sTemp As String
sTemp = UCase(Replace(Replace(Replace(Replace( _
sInput, "A", "u"), "C", "g"), "G", "c"), "U", "a"))
ReverseComplement = StrReverse(sTemp)
End Function

On Mon, 17 Jan 2005 11:43:12 -0700, JE McGimpsey
wrote:

Perhaps

Public Function ReverseComplement(sInput As String)
Dim sTemp As String
sTemp = UCase(Replace(Replace(Replace(Replace( _
sInput, "A", "u"), "C", "g"), "G", "c"), "U", "a"))
ReverseComplement = sTemp
End Function



In article ,
M H wrote:

I've written an excel function aim to change a RNA sequence to its
reverse complement (e.g. from "ACGUUGUA" to "UACAACGU") as:

Function ReverseComplement(Rcell As Range, Optional IsText As
Boolean)

Dim i As Integer
Dim strReverseSeq As String
Dim strSenseSeq As String

strSenseSeq = Trim(Rcell)

For i = 1 To Len(strSenseSeq)
strReverseSeq = Mid(strSenseSeq, i, 1) & _ strReverseSeq
Next i

If IsText = False Then
ReverseComplement = CLng(strReverseSeq)
Else
ReverseComplement = strReverseSeq
End If

strSeqA1 = Replace(strReverseSeq, "A", "1")
strSeqC2 = Replace(strSeqA1, "C", "2")
strSeqG3 = Replace(strSeqC2, "G", "3")
strSeqT4 = Replace(strSeqG3, "U", "4")
strSeq1T = Replace(strSeqT4, "1", "U")
strSeq2G = Replace(strSeq1T, "2", "G")
strSeq3C = Replace(strSeq2G, "3", "C")
strSeq4A = Replace(strSeq3C, "4", "A")

End Function

The first half works fine, which reverse the sequence, but the
second
part doesn't work, which cannot make the comoplements Please help
for
debug. Much thanks.

*** Sent via Developersdex http://www.developersdex.com ***
Don't just participate in USENET...get rewarded for it!

Thanks for the explanation.

--
Regards,
Tom Ogilvy

"GysdeJongh" wrote in message
...
Hi,
sorry did not find the original posting so I answer this one.
I see how you reverse the strand .
I do not understand how you want to complement the strand.
So I can not comment your solution.
But have a solution for the problem if you want.
Feel free to adapt it to your needs.

'This function converts a DNA string to its
'reverse complement
'Gys de Jongh 16-jun-1999
Function Rev(Forw As String) As String
Dim ForwA(1 To 100) As String * 1
Dim RevA(1 To 100) As String * 1
N = Len(Forw)
If N 100 Then
Rev = "Input too long (max 100)"
Exit Function
End If
For I = 1 To N
ForwA(I) = Mid(Forw, I, 1)
Next I
For I = 1 To N
Select Case ForwA(N - I + 1)
Case "A"
RevA(I) = "T"
Case "a"
RevA(I) = "t"
'From A to T
Case "C"
RevA(I) = "G"
Case "c"
RevA(I) = "g"
'From C to G
Case "G"
RevA(I) = "C"
Case "g"
RevA(I) = "c"
'From G to C
Case "T"
RevA(I) = "A"
Case "t"
RevA(I) = "a"
'From T to A
Case Else
RevA(I) = "N"
'Rest is N
End Select
Next I
For I = 1 To N
Rev = Rev & RevA(I)
Next I
End Function

Short explanation for Tom :
DNA contains the information for cells
It is a double helix with 2 strings , molecules
The two strings contain the same information
They are redundant , one can be used to construct the other
In each string A only pairs with T and C only with G
But :
the Sense strand reads from left to right and
the anti Sense strand from right to left
so :

ACGTCCCTGAAATT <====Sense strand
TGCAGGGACTTTAA <====anti Sense strand

Finding the reverse complement means finding the other if one is known

hth
Gys




"Tom Ogilvy" wrote in message
...
As an example
Assume you had a reversed string like AAA

your code would convert it like this

AAA = 111 = UUU

If that is what you want, then Ok. If the problem is you would want 111
as
a result, then I think you need to go to an intermediate stage (two step
process)

AAA = MMM = 111

Where the middle stage would use unique identifiers so you wouldn't
convert
any value after it was converted to a final value.

A to M, M to 1
C to N, N to 2
G to O, O to 3
U to P, P to 4
1 to Q, Q to U
2 to R, R to G
3 to S, S to C
4 to T, T to A

--
Regards,
Tom Ogilvy



"M H" wrote in message
...

I've written an excel function aim to change a RNA sequence to its
reverse complement (e.g. from "ACGUUGUA" to "UACAACGU") as:

Function ReverseComplement(Rcell As Range, Optional IsText As Boolean)

Dim i As Integer
Dim strReverseSeq As String
Dim strSenseSeq As String

strSenseSeq = Trim(Rcell)

For i = 1 To Len(strSenseSeq)
strReverseSeq = Mid(strSenseSeq, i, 1) & _ strReverseSeq
Next i

If IsText = False Then
ReverseComplement = CLng(strReverseSeq)
Else
ReverseComplement = strReverseSeq
End If

strSeqA1 = Replace(strReverseSeq, "A", "1")

here strSeqA1 etc are just a not declared variables which don't seem to
reach
the output of the function ????

strSeqC2 = Replace(strSeqA1, "C", "2")
strSeqG3 = Replace(strSeqC2, "G", "3")
strSeqT4 = Replace(strSeqG3, "U", "4")
strSeq1T = Replace(strSeqT4, "1", "U")
strSeq2G = Replace(strSeq1T, "2", "G")
strSeq3C = Replace(strSeq2G, "3", "C")
strSeq4A = Replace(strSeq3C, "4", "A")

End Function

The first half works fine, which reverse the sequence, but the second
part doesn't work, which cannot make the comoplements Please help for
debug. Much thanks.

*** Sent via Developersdex http://www.developersdex.com ***
Don't just participate in USENET...get rewarded for it!

Much thanks to JE's original idea, precise and concise, and Myrna's
essential amendment. Actually I realize my stupidity of missing one
line as Tom suggested when I was on the bed, and I'm really amazed to
see the how several brains led to the one-line code!

This is finally what I've to achieve, with including the degenerate
alphabets and distinguishing DNA from RNA:

Public Function RevCompl(sInput As String)

Dim sTemp As String

sUInput = UCase(sInput)
sTemp1 = Replace(sUInput, "T", "")

'If it is DNA
If Len(sTemp1) < Len(sUInput) Then
sTemp = Replace(Replace(Replace(Replace(Replace(Replace( _
Replace(Replace(Replace(Replace(Replace(Replace( _
sUInput, "R", "y"), "M", "k"), "Y", "r"), "K", "m"), _
"H", "d"), "D", "h"), "B", "v"), "V", "b"), _
"A", "t"), "C", "g"), "G", "c"), "T", "a")
'if it is RNA
Else
sTemp = Replace(Replace(Replace(Replace(Replace(Replace( _
Replace(Replace(Replace(Replace(Replace(Replace( _
sUInput, "R", "y"), "M", "k"), "Y", "r"), "K", "m"), _
"H", "d"), "D", "h"), "B", "v"), "V", "b"), _
"A", "u"), "C", "g"), "G", "c"), "U", "a")
End If

RevCompl = StrReverse(UCase(sTemp))

End Function


rgds,
Maurice

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Hi,
you are right , thank you very much for this suggestion. The job is to reverse
the string and replace A by T etc. It is called : calculating the Reverse
Complement in bioinformatics. There is of course dedicated software. Look here
if you like to see an example :

http://www.mbio.ncsu.edu/BioEdit/bioedit.html


I made this little piece of VBA to calculate the reverse complement for a very
large number of short sequences.

Your solution is more elegant and probably faster. It did not occur to me that
it can be done that way because I am in genetics and statistics . I am not a
programmer.
Thanks again for your time
Gys





"Myrna Larson" wrote in message
...
I believe By Complement, he means interchange A and T and C and G, as you (and
he) are doing.

But why do you not want to use Replace, StrReverse and UCase$? The code is
much shorter -- it can be reduced to just 7 lines.

On Mon, 17 Jan 2005 23:56:04 +0100, "GysdeJongh" wrote:

Hi,
sorry did not find the original posting so I answer this one.
I see how you reverse the strand .
I do not understand how you want to complement the strand.
So I can not comment your solution.
But have a solution for the problem if you want.
Feel free to adapt it to your needs.

'This function converts a DNA string to its
'reverse complement
'Gys de Jongh 16-jun-1999
Function Rev(Forw As String) As String
Dim ForwA(1 To 100) As String * 1
Dim RevA(1 To 100) As String * 1
N = Len(Forw)
If N 100 Then
Rev = "Input too long (max 100)"
Exit Function
End If
For I = 1 To N
ForwA(I) = Mid(Forw, I, 1)
Next I
For I = 1 To N
Select Case ForwA(N - I + 1)
Case "A"
RevA(I) = "T"
Case "a"
RevA(I) = "t"
'From A to T
Case "C"
RevA(I) = "G"
Case "c"
RevA(I) = "g"
'From C to G
Case "G"
RevA(I) = "C"
Case "g"
RevA(I) = "c"
'From G to C
Case "T"
RevA(I) = "A"
Case "t"
RevA(I) = "a"
'From T to A
Case Else
RevA(I) = "N"
'Rest is N
End Select
Next I
For I = 1 To N
Rev = Rev & RevA(I)
Next I
End Function

Short explanation for Tom :
DNA contains the information for cells
It is a double helix with 2 strings , molecules
The two strings contain the same information
They are redundant , one can be used to construct the other
In each string A only pairs with T and C only with G
But :
the Sense strand reads from left to right and
the anti Sense strand from right to left
so :

ACGTCCCTGAAATT <====Sense strand
TGCAGGGACTTTAA <====anti Sense strand

Finding the reverse complement means finding the other if one is known

hth
Gys





"Tom Ogilvy" wrote in message
...
As an example
Assume you had a reversed string like AAA

your code would convert it like this

AAA = 111 = UUU

If that is what you want, then Ok. If the problem is you would want 111 as
a result, then I think you need to go to an intermediate stage (two step
process)

AAA = MMM = 111

Where the middle stage would use unique identifiers so you wouldn't convert
any value after it was converted to a final value.

A to M, M to 1
C to N, N to 2
G to O, O to 3
U to P, P to 4
1 to Q, Q to U
2 to R, R to G
3 to S, S to C
4 to T, T to A

--
Regards,
Tom Ogilvy



"M H" wrote in message
...

I've written an excel function aim to change a RNA sequence to its
reverse complement (e.g. from "ACGUUGUA" to "UACAACGU") as:

Function ReverseComplement(Rcell As Range, Optional IsText As Boolean)

Dim i As Integer
Dim strReverseSeq As String
Dim strSenseSeq As String

strSenseSeq = Trim(Rcell)

For i = 1 To Len(strSenseSeq)
strReverseSeq = Mid(strSenseSeq, i, 1) & _ strReverseSeq
Next i

If IsText = False Then
ReverseComplement = CLng(strReverseSeq)
Else
ReverseComplement = strReverseSeq
End If

strSeqA1 = Replace(strReverseSeq, "A", "1")
strSeqC2 = Replace(strSeqA1, "C", "2")
strSeqG3 = Replace(strSeqC2, "G", "3")
strSeqT4 = Replace(strSeqG3, "U", "4")
strSeq1T = Replace(strSeqT4, "1", "U")
strSeq2G = Replace(strSeq1T, "2", "G")
strSeq3C = Replace(strSeq2G, "3", "C")
strSeq4A = Replace(strSeq3C, "4", "A")

End Function

The first half works fine, which reverse the sequence, but the second
part doesn't work, which cannot make the comoplements Please help for
debug. Much thanks.

*** Sent via Developersdex http://www.developersdex.com ***
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Hi,
very nice solution. I have one question : should there be a test on the lenght
of the sInput srting or is there no 65k restriction ?

Gys


"M H" wrote in message
...
Much thanks to JE's original idea, precise and concise, and Myrna's
essential amendment. Actually I realize my stupidity of missing one
line as Tom suggested when I was on the bed, and I'm really amazed to
see the how several brains led to the one-line code!

This is finally what I've to achieve, with including the degenerate
alphabets and distinguishing DNA from RNA:

Public Function RevCompl(sInput As String)

Dim sTemp As String

sUInput = UCase(sInput)
sTemp1 = Replace(sUInput, "T", "")

'If it is DNA
If Len(sTemp1) < Len(sUInput) Then
sTemp = Replace(Replace(Replace(Replace(Replace(Replace( _
Replace(Replace(Replace(Replace(Replace(Replace( _
sUInput, "R", "y"), "M", "k"), "Y", "r"), "K", "m"), _
"H", "d"), "D", "h"), "B", "v"), "V", "b"), _
"A", "t"), "C", "g"), "G", "c"), "T", "a")
'if it is RNA
Else
sTemp = Replace(Replace(Replace(Replace(Replace(Replace( _
Replace(Replace(Replace(Replace(Replace(Replace( _
sUInput, "R", "y"), "M", "k"), "Y", "r"), "K", "m"), _
"H", "d"), "D", "h"), "B", "v"), "V", "b"), _
"A", "u"), "C", "g"), "G", "c"), "U", "a")
End If

RevCompl = StrReverse(UCase(sTemp))

End Function


rgds,
Maurice

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It's probably the terminology that's used in the genetics/biology community.

On Mon, 17 Jan 2005 19:18:55 -0500, "Tom Ogilvy" wrote:

Bad choice of words.

Thx ,
nice piece of code to do the check
32k is enough for most genes :)
Gys


"Peter T" <peter_t@discussions wrote in message
...
Hi Gys

Someone may advise what the ultimate limit is but try for your self:

Sub test()
Dim s As String, s2 As String, n As Long, s2

s = "ACGT"
For n = 1 To 15 ' 15 len 64k, 17 len 512k
s = s & s
Next

s2 = RevCompl(s)

MsgBox Len(s) & " " & Left(s, 12) & vbCr & _
Len(s2) & " " & Left(s2, 12)

End Sub

But note cells can only store strings up to 32k.

Regards,
Peter T


"GysdeJongh" wrote:
Hi,
very nice solution. I have one question : should there be a test on the
lenght
of the sInput srting or is there no 65k restriction ?

Gys


"M H" wrote in message
...
Much thanks to JE's original idea, precise and concise, and Myrna's
essential amendment. Actually I realize my stupidity of missing one
line as Tom suggested when I was on the bed, and I'm really amazed to
see the how several brains led to the one-line code!

This is finally what I've to achieve, with including the degenerate
alphabets and distinguishing DNA from RNA:

Public Function RevCompl(sInput As String)

Dim sTemp As String

sUInput = UCase(sInput)
sTemp1 = Replace(sUInput, "T", "")

'If it is DNA
If Len(sTemp1) < Len(sUInput) Then
sTemp = Replace(Replace(Replace(Replace(Replace(Replace( _
Replace(Replace(Replace(Replace(Replace(Replace( _
sUInput, "R", "y"), "M", "k"), "Y", "r"), "K", "m"), _
"H", "d"), "D", "h"), "B", "v"), "V", "b"), _
"A", "t"), "C", "g"), "G", "c"), "T", "a")
'if it is RNA
Else
sTemp = Replace(Replace(Replace(Replace(Replace(Replace( _
Replace(Replace(Replace(Replace(Replace(Replace( _
sUInput, "R", "y"), "M", "k"), "Y", "r"), "K", "m"), _
"H", "d"), "D", "h"), "B", "v"), "V", "b"), _
"A", "u"), "C", "g"), "G", "c"), "U", "a")
End If

RevCompl = StrReverse(UCase(sTemp))

End Function


rgds,
Maurice

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