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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