CLONEMATE 'READ ME' FILE ST VERSION ===================================== Date: 89-10-16. Author: Keith L. Steward Univ: Dept. Microbiology & Immunology, University of Western Ontario, London, Ontario, Canada N6A 5C1 ph.# (519) 661-2111 ext 6618 Home: 120 Cherryhill Drive, Apt 610 London, Ontario, Canada N6H 4N9 ph.# (519) 663-9285 E-mail: GEnie-- send to 'K.STEWARD' Compuserve-- send to '73707,3407' BITNET-- send to 'KSTEWARD@NRCCAD.NRC.CA' --------------------------------- CLONEMATE is a public domain DNA sequence analysis/cloning program for the Atari ST and the MSDOS PC. It is by no means a complete and finished sequence analysis package, but what it does do, I think you will agree, it does very well and very fast. I intended the program to more of a tool for designing cloning experiments than a program for doing homology/similarity analyses. Because of this most of the program's functions relate to finding and showing restriction sites, predicting fragments, manipulating enzyme data, and editing sequences. The homology functions while offering some flexibility are not nearly as extensive as those offered by commericially available software. This package should contain at least the following files: CLONMATE.TOS -the program RENZYME.DAT -the restriction enzyme data CLONMATE.DOC -the uncomplete user's manual READ_ME.1ST -this file! But may also contain ST version of the Lattice 'C' code miscellaneous GENBANK format sequence files Please note that I haven't finished the user's manual but I hope to sometime in the near future. Nevertheless, I think you will find CLONEMATE very easy to use and shouldn't have too many problems figuring out how it works. ST user's may be a little disappointed that the program is not GEM based. But there are several good reasons why this is so: While I have done some GEM programming, my talents in this area still need some honing. Non-GEM programs, ie. TEXT-only programs, are orders of magnitude easier and faster to write, which allowed me for example to write and test about 50% of CLONEMATE during my '88 Christmas holidays. Another reason the program is text-based is that this allows me to very easily port CLONEMATE to almost any machine, including of course the ubiquitous MSDOS PC. Only slight changes in the C code were necessary to compile and run the software on the PC. Take heart though, ST user's, if enough of you desire it, I may make an effort to develop a graphic-based, CAD-like version (more like a complete re-write!) of CLONEMATE, with perhaps multi-level zooming, automatic vector/construct illustration and printing, point & click & dragging of restriction fragments to construct new sequences, etc, etc, etc. Future versions of the text-based CLONEMATE will also be exciting. I have unlimited ideas and good C programming skills for improving the package, but unfortunately very limited spare time (I wrote nearly all of CLONEMATE while doing a Master's, but now I'm doing a PhD!). Here is a very incomplete list of features I would like to add: o much more flexible choice of enzymes to use in the analyses: a) specify by fragment end structure produced, eg. 5' overhangs, 3' overhangs, or blunt ends b) specify by minimum size of recogn. seq. (already does this!) c) type in a list of only the enzymes to be used d) specify the maximum number of cut sites allowed e) specify if enzymes with variable/multiple recognition sequences are to be avoided f) only use enzymes which cut outside of a certain region (eg. a gene to be cloned) g) a combination of these (eg. only 5' overhang producers with 6 bp or larger recogn. seq. which cut outside of a gene region) o when loading or saving sequences, user should be able to view the disk directory o a restriction fragment-based editor, in which the user constructs a new sequence by specifying an existing sequence, the enzymes to digest it with, and choosing one or more of the resulting fragments, after perhaps processing the end (eg filling in, or trimming back). This would allow one to quickly simulate what one is doing in the lab and have a recombinant sequence with which to devise screening strategies, etc. o the annotation data that is part of a GENBANK entry should be made use of and when edits are done (eg. new constructs) this data should be adjusted automatically to reflect the edits. o retrieve sequences from the compressed GENBANK files. o very flexible formatted printouts of sequences (ie. variations in numbering, spacing etc.) o * a cloning scheme searcher * I really like this one! A user could just specify the approximate region (+ or - so many bp), the cloning vector to be used, and then this function would compile a list of usable restriction sites flanking the region to be cloned and those which are compatible (ligatable) and unique in the vector, and then proceed to evaluate sets of cloning sites based on criteria such as size of cloned region (can it be separated and cut from a gel?), cost of the enzyme, enzymes which use the same buffer, enzymes which do not have quirks, etc.... Get the picture? With such a function one could I think, have a list cloning schemes within minutes which are ranked according to feasibility and the cloning criteria. o versatile homology comparison, and GENBANK homology searching functions o any other ideas CLONEMATE user's might suggest to me. o etc, etc, etc, .... I could go on and on. But the point is, if enough user's desire these features I could justify spending more of my precious spare time incorporating them and evolve CLONEMATE into an extremely useful cloning tool for all to use. For this reason, I would very much like to compile a list of CLONEMATE user's and their comments. Please let me know if you are using CLONEMATE and give me some feedback about the program and what features you wish to see so that together we can improve it. Keith L. Steward