Fasta on Mac

Richard Cooke cooke at univ-perp.fr
Mon Jan 10 02:31:47 EST 1994


Jeroen Coppieters wrote:

>I downloaded fasta16c24b.shar.Z. the documentation (fasta16.doc) mentions 
>that this program should run on Macintosh, but does not indicate which
>C-compiler it is compatible with. There is no installation chapter
>for Mac (there is for PC and Unix)
>Is there a version available with Mac specific instructions for 
>installation?
>I would like to use the program together with the EMBL CD-ROM
>Has anybody done this?

If things haven't changed, and in contrast to the PC or UNIX versions, you
need to order the Mac programs from Bill Pearson (Dept. of Biochemistry, U.
of Virginia, Charlottesville VA). They used to cost 60 dollars. They work
fine with the CD-ROM from EMBL. All you need to do is to alter the fastgbs
file to point to the disk. The big problem is the time taken for the
alignments. Before we moved to network alignments and a UNIX machine, it
took about twenty minutes for a protein alignment against Swiss-Prot
(ktup=2) and several _hours_ for a nucleotide alignment, but we transferred
the SP and EMBL files to a 1-giga hard disk. If I remember rightly, using
the CD-ROM took at least twice as long! If you really want to do fasta
alignments, particularly of nucleotides, you could always look at the EMBL
server (send a "help" to fasta at embl-heidelberg.de).

        Richard Cooke 

       ****************************************************
       *                                                  *
       *     Richard Cooke                                *
       *    Laboratoire de Biologie Moleculaire Vegetale  *
       *    Universite de Perpignan                       *
       *    cooke at univ-perp.fr                            *
       ****************************************************






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