Fwd: [Biococoa-dev] Digest tool
Alexander Griekspoor
mek at mekentosj.com
Sun Feb 27 07:58:03 EST 2005
Correction, I only have the binary of the restrictionmapper plugin John
wrote, not the source. Perhaps he can send you the source (and me,
because I would like to have the source as well ;-). John?
Cheers,
Alex
Begin forwarded message:
> From: Alexander Griekspoor <mek at mekentosj.com>
> Date: 27 februari 2005 13:55:00 GMT+01:00
> To: Koen van der Drift <kvddrift at earthlink.net>
> Cc: BioCocoa Mailinglist <biococoa-dev at bioinformatics.org>
> Subject: Re: [Biococoa-dev] Digest tool
>
> Hmm, in principle there are many similarities so yes, we should try to
> make it work with DNA as well (don't know much about RNA cutting
> enzymes and their specificity...
> Don't want to sound to commercial (well, it's freeware anyway), but
> perhaps you can download our program EnzymeX
> (http://www.mekentosj.com/enzymex ) and play a bit with it. Also, Tom
> added in the help files quite some info on how these enzymes work.
> Finally, we have added a piece on our website about it:
> http://www.mekentosj.com/enzymex/science.html
> Some potential pitfalls we have to foresee in the method:
> - DNA has two strands and enzymes can both generate blunt ends and
> overhangs (cut different position in the forward and reverse strand,
> see the picture of the enzyme sequence in enzymeX).
> - Far more than is the case in peptide cleavage, ambiguity place a
> major role in DNA restriction enzymes: i.e. enzymes like EaeI that
> recognises: y^GGCCr
> - DNA can be circular, meaning that one has to account for potential
> cuts in the connecting segment if circularity is the case
> - Later on we can add the problem of methylation sensitivity, but
> that's way more advanced.
> I know John has created a DNA digestion plugin for 4Peaks, so he can
> tell you more probably. I'll send you the source off-list...
> Cheers,
> Alex
>
> On 27-feb-05, at 5:17, Koen van der Drift wrote:
>
>> Hi,
>>
>> I am going to work on the BCToolDigest class and need some feedback
>> from the DNA/RNA folks. I already have code to digest a protein, and
>> can add that without much problems. However, I would like to try to
>> make the class as universal as possible, so it should also work for
>> DNA and RNA. The code that I already have will digest a protein,
>> based on information of an enzyme that is stored in a plist file. An
>> example is:
>>
>> <key>Trypsin</key>
>> <dict>
>> <key>CleaveAt</key>
>> <string>KR</string>
>> <key>DontCleaveAdjacentTo</key>
>> <string>P</string>
>> <key>CleaveDirection</key>
>> <string>C</string>
>> </dict>
>>
>> So it defines the name of the enzyme in the key, and then identifies
>> where to cleave the protein, in this case at a lysine or arginine
>> residue. The string can contain more than one residues. It also adds
>> the possibility to define a residue that inhibits the cleavage if it
>> is adjacent to the given residue(s). Finally it defines on which side
>> of the residue to cleave.
>>
>> So my question is, when digesting an DNA/RNA, can I use a similar
>> approach? I have absolutely no clue about the digestion of DNA/RNA,
>> so the mechanism could well be completely different. In that case
>> additional class needs to be written, and maybe a super class to hold
>> code that is in common.
>>
>> The result of the code I already have is an array of subsequences.
>> Will the result of a DNA/RNA digest be similar?
>>
>> thanks,
>>
>> - Koen.
>>
>> _______________________________________________
>> Biococoa-dev mailing list
>> Biococoa-dev at bioinformatics.org
>> https://bioinformatics.org/mailman/listinfo/biococoa-dev
>>
>>
> *********************************************************
> ** Alexander Griekspoor **
> *********************************************************
> The Netherlands Cancer Institute
> Department of Tumorbiology (H4)
> Plesmanlaan 121, 1066 CX, Amsterdam
> Tel: + 31 20 - 512 2023
> Fax: + 31 20 - 512 2029
> AIM: mekentosj at mac.com
> E-mail: a.griekspoor at nki.nl
> Web: http://www.mekentosj.com
>
> Claiming that the Macintosh is inferior to Windows
> because most people use Windows, is like saying
> that all other restaurants serve food that is
> inferior to McDonalds
>
> *********************************************************
>
> _______________________________________________
> Biococoa-dev mailing list
> Biococoa-dev at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/biococoa-dev
>
>
*********************************************************
** Alexander Griekspoor **
*********************************************************
The Netherlands Cancer Institute
Department of Tumorbiology (H4)
Plesmanlaan 121, 1066 CX, Amsterdam
Tel: + 31 20 - 512 2023
Fax: + 31 20 - 512 2029
AIM: mekentosj at mac.com
E-mail: a.griekspoor at nki.nl
Web: http://www.mekentosj.com
The requirements said: Windows 2000 or better.
So I got a Macintosh.
*********************************************************
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