wrp@biochsn.acc.virginia.edu (William R. Pearson) (06/21/88)
Recently, David Lipman and I published a paper describing improved
programs for DNA and protein sequence analysis in PNAS (1988) 85:2444.
This is a large group of programs, called the FASTA package, that
replace the older FASTP and FASTN library search programs. The FASTA
package includes the FASTA and TFASTA programs for database
searches, LFASTA and PLFASTA for local similarity searches and plots,
RDF2, and a large number of programs that were not described in
the PNAS paper. These other programs include ALIGN, a program for
rigorous global alignment using code from Gene Myers and Webb Miller,
GARNIER, GREASE, and TGREASE, programs for examining protein structure,
and other programs for extracting sequences from libraries,
calculating amino acid compositions, etc.
These programs are written in 'C' and have been tested under UNIX
Sys V, SUN OS (4.3 BSD), Xenix, VAX/VMS, DOS, and on the MacIntosh.
The FASTA package does not include any sequence databases, but
versions of the program work with the NBRF/PIR protein and DNA sequence
databases on VAX/VMS computers, libraries in the U. Wisconsin
Genetics Computer Group format, and sequence libraries in the
GENBANK compressed floppy disk format on the IBM-PC and unix
machines.
Since this group of programs runs on a large variety of
computers, copies of the program are available in a variety of forms.
UNIX FTP
The simplest way to get the FASTA package is by
anonymous ftp from the ARPANET host uvaarpa.Virginia.EDU. If
your university has arpanet access, you should try this
first. From a machine that has access to the ARPANET, type:
ftp uvaarpa.Virginia.EDU
or alternatively
ftp 128.143.2.7
and login with the user Name: anonymous
and a Password: your_userid
The FASTA package is in the file public_access/fasta.shar. To
transfer the file:
cd public_access
get fasta.shar fasta.shar
This is a unix "shar" file, which means that on a
unix machine, you can type:
sh fasta.shar
and the fasta.shar file will be broken into the files required
to recompile fasta programs. A "Makefile" is included for Sun
(4.2BSD), ATT SysV, and Xenix flavors of unix. Another
"makefile" is included for Turbo 'C' on the IBM-PC, and a third
is included for the VMS operating system on a VAX. If you
copy the programs from uvaarpa, please send a mail message to
"wrp@Virginia.EDU" with your name and address (or e- mail
address) so that I can keep track of who has the program, and
inform you of any bugs that may crop up.
VAX/VMS
If you are planning to use these programs on a VAX/VMS
computer, you should get a VAX/VMS backup tape directly from
me. There is no charge for the tape, but I ask that you copy
the files from the tape and return it to me as soon as
possible. Please do not send me tapes, as it is much
easier for me to make a large number of tapes and recycle them
than it is to make individual tapes.
UNIX If you do not have ARPANET access but are running
UNIX, I can make a UNIX tar tape with the fasta.shar file, or I
can write 60 Mbyte SUN cartridges. Again, please do not send
me a tape, just return the one I send you, promptly.
IBM-PC The FASTA package comes on three 5 1/4 floppy disks
for the IBM-PC, and includes complete source code and executable
versions of the programs, and also *.BGI graphics device
driver programs from Borland's Turbo 'C' package. I am charging
$60.00 US for the PC version of the program, please send
checks to:
William R. Pearson
1611 Westwood Rd.
Charlottesville, VA 22901
There is a $25.00 additional charge for purchase ord-
ers.
Macintosh
The FASTA package is also running on the Macintosh computer,
although the program is not very "Mac-like". I expect to
be distributing the Macintosh version by June 1. The Mac
version will also cost $60.00 US, please send checks to the
address above.
Sequence Libraries
If you are getting the FASTA package for use on an IBM-PC
or Macintosh, I can also provide the NBRF-Protein sequence library.
I only provide the sequence portion of the library, if you need the
annotations, you should arrange to get an account on the NBRF-PIR
computer, or on BIONET. A single copy of the library costs $50 (7
IBM-PC disks as of release 16, 31-March-1988), a one year
subscription (the library and 3 updates as they come out) costs
$200. Please add $25 for purchase order processing. The protein
sequence library on Macintosh disks costs $75.00, a one year sub-
scription is $300. Overseas orders for the protein sequence library
should add $10 for one copy, $40.00 for a one-year subscription (4
copies).
(Please note: Some you have subscribed to the pro-
tein sequence library in the past, and received a
note saying that I was no longer distributing the
library. Well, I've changed my mind, and have de-
cided to go back to diskette duplication.)
The GENBANK DNA sequence library is available for the IBM-PC
and the Macintosh from:
GenBank
c/o Intelligenetics
700 E. El Camino Real
Mountain View, CA 94040 USA
They charge $125 - $175 for release 55.0 of the library, depending
on the method of payment, and the disk format requested.
If you need a VAX/VMS 9-track tape or a UNIX 9-track tape or 60
Mbyte cartridge, please write me at:
Department of Biochemistry
Box 440 Jordan Hall
U. of Virginia
Charlottesville, VA 22908
or send me electronic mail at: wrp@virginia.EDU, wrp@virginia.BITNET,
or ...!uunet!virginia!wrp. Please do not send me any tapes or
diskettes.
William R. Pearson
wrp@virginia.EDU