Can DNAsis replace GCG package? Or almost??

A428ENDE at VM1.SARA.NL A428ENDE at VM1.SARA.NL
Thu Oct 6 09:28:04 EST 1994


In article <36vkk9$gtq at mace.cc.purdue.edu>
xniu at mace.cc.purdue.edu (Xiaomu Niu) writes:
 
>        We narrowed our choices down to two:
>                (1) a 486/586 pc running linux and X-windows
>                (2) a Machintosh or a Power Mac
>
>        With the first one, we can run MS-Windows with Hitachi's
>DNAsis for window, or we install Linux and run GDE plus other freely
>availabe sequence analysis programs for unix, something like BIRCH
>(but running on a pc).
 
Although we bought DNAsis on a Mac, I still believe that we made the wrong dess
ision. With a 586 (which is much cheaper than a PowerMac 8100) you can indeed r
un linux and take advantage of all the software available in the Unix environme
nt and you have a very fast PC with all the advantages and programs in this env
ironment (there are also a lot of Public domain and Shareware available).
 
>        With the second choice, we probably have to purchase the
>MacDNAsis from Hitachi. Or we can try GeneWorks (?) also.
>
>        But here is the question: (sorry for the long introduction)
>Can DNAsis replace GCG completely or nearly? What about speed? It
>seems we have people here running DNAsis on a Mac SE with a CD-ROM
>happily. If we understand right, GDE covers most of GCG's functions,
>and it's available for free.
 
Don't buy the Hitachi MacDNAsis! It is full of bugs and strange things. For exa
mple sometimes you can use small letters in your sequence (handy if you are alm
ost sure that this is the base you read) but it converts them randomly to upper
case. In the contig manager it has a very strange way of aligning the sequences
 and sometimes ruin your files by introducing hyphens (it can do it in the mult
iple but it does it also in your sequences!). Complement, reverse and reverse +
complement are not what you expect and so on. It has no ways to format the outp
ut of all the operations so everything must be done in a drawing program or tex
t editor. And I feel that I don't have all the possibilities which were impleme
nted in GCG (for example blast). Does someone have the email number of Hitachi,
 because they are very hard to reach from Europe.
 
>        Please respond to this account or post here. If there is
>enough interest, I'll glad to post a summary.  Thank you in advance.
 
Please do. May be we can also invest in something better.
Henk van de Kamer
CHLAMY at SARA.NL




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