[ANNOUNCE] CloneIt Finding cloning strategies

Pierre Lindenbaum lindenb at jouy.inra.fr
Tue Aug 25 02:26:37 EST 1998


: :      _________________________________________________________________
: :    
: :                                     CLONEIT

: :  AN ANSI-C PROGRAM FINDING SUB-CLONING STRATEGIES, IN-FRAME DELETIONS AND
: :        FRAMESHIFTS USING RESTRICTION ENZYMES AND DNA POLYMERASES.

: (i) The example sequence and other files cited on the web page are not
: in standard Unix format, i.e., they have some weird end-of-line
: markers, so you have to hack them to make the files readable on Unix
: systems or the program hangs. Surely it's better to reformat the
: linked files in standard Unix format at the web page end?

	Thank you for your post. I'm currently writing a new version of 
	CloneIt which will have a few bugs (Sorry about  this !) which
	will be able to handle more files format (including binary files
	from DNA STrider), to browse the strategies (go next, previous..)
	etc...

: (ii) I tried using the "project" file input as described on the web
: page. Got a segmentation fault at the line for "set.vector.atg".

	Thank you ! I'll correct this in the new version.
	I don't use a lot the "project" option ( this was a wish of
	one of my  reviewers)

: Correct that and 9 other similar lines and the project file "set.*"
: statements now work properly.


: (iv) The documentation does not make it very clear how you use the
: program to clone a random section of plasmid A into a random section of
: plasmid B.

	The program finds the polylinkers boundaries using the small provided
	database called "Polylinkers.Set".

It can be worked out, but more examples would be a great
: help.  Otherwise people will think it can only be used for specialised
: two-hybrid system type subcloning.

	And It's not ! :-)


: Having said that, I was pleased to see that in the first example of
: subcloning with plasmids of mine that I gave it, the strategy first
: suggested was the one I'd found the hard way myself.

	Thank you for this advertising !


: Best wishes,

: Chris Boyd PhD                 MRC Human Genetics Unit, Western General Hospital
: Christopher.Boyd at hgu.mrc.ac.uk           Crewe Road, Edinburgh EH4 2XU, Scotland
: http://www.hgu.mrc.ac.uk/Users/Christopher.Boyd/  T/F: +44(0)131 3322471/3432620

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   CloneIt WWW Home Page:http://locus.jouy.inra.fr/soft/cloneit/cloneit.html




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