farrah@nwnexus.WA.COM (Theresa Farrah) (01/03/90)
I am trying to gather information on sequence analysis software for the Mac. Currently, our company uses UWGCG software, but all of our scientists have Macintoshes and would prefer to use their Macs for sequence analysis. I am aware of the MacVector from IBI, but the price seems prohibitive ($2500) given that we have about 30 users, each of whom would want the software on their own Mac. Right now I am interested only in general-purpose software -- programs that do many things ranging from restriction mapping to alignments and homology searches. If anyone is aware of such software, let me know and I'll post a summary of the responses. Terry (farrah@nwnexus.wa.com)
V5222E@templevm.bitnet (Win Hide) (01/05/90)
Mac Software available commercially includes: DNA inspector (latest version is good) PLasmid draw (good but pricey) Full packages are sparse, the newest coming to mind is the Mac version of PC gene from Intelligenetics or the most likely to be out soon is the package from IBI (the name escapes me) going for $2500 etc,.... I have resorted to using a collection of single purpose porograms, and find thi s ok, as long as cut and paste keeps working, we'll all be fine. Examples are: DNA ID (available from EMBL via Email) Stryder 1.0 (I have a PD copy and you are welcome to it, just write) I am looking for a good alignement program, and have yet toi fnd one. But that usually eats speed and memeory, so is better suited for a vax package such as the Wisconsin package if you can get online to it. Write for more details. Also homology searching implies you have some kind of dtatabase locally. If it is Genbank or wotever, the better bet is to access genbank at Bionet (intelligenetics) which has the very lates uploads, and to use FastA to search via FTP. This sounds complicated, but in fact is very simple. IE: The best mac program for all of this is probably RedRyder!! I have also been looking for Macprogs and get by as stated. My biggest hassle right now is aligning stuff. There is a PD IBM program available from EMBL, I currently use that, then port to a mac for the fun bits (I also use PAUP which is for phgylogenetic analysis on the MAc). Best of luck and let us know wot is available out there... Win Hide Temple University Biology Dept. 215 787 6688
lehvaslaiho@cc.helsinki.fi (01/05/90)
In article <9001042152.AA10439@net.bio.net>, V5222E@templevm.bitnet (Win Hide) writes: > I currently use that, then port to a mac for the fun bits (I also use > PAUP which is for phgylogenetic analysis on the MAc). Where to get a copy of PAUP? Is it commercial or free? -------------------- Since I am writing to this forum, I might as well mention a good sequence analysis program: A company called "Soft Gene Berlin" (or close to that, they have recently changed the name) has a program called MacMolly. They sell it for DM 1320 (or equivalent of US$) a copy plus DM 680 for additional copies. It consists of four applications (Enter&List, Compare, Restrict and Translate) which together do almost everything imaginable. They also have an ultra-fast EMBL sequence database application for DM 5250. The best part in using MacMolly is that by telling the company what you want, you will get the feature in the next version in few mounths. That is the way it worked for me, anyway. Also, for us in Europe, they are comfortably close. The address is: Dr. Burghardt Wittig Soft Gene Berlin Offenbacher Strasse 5 D-1000 Berlin 33 Tel.: 030/8211407 Fax: 030/8219764
B_FOLEY@uvmvax.bitnet (01/06/90)
Indiana University provides a wealth of Macintosh software
for molecular biologists. Don Gilbert (GILBERTD@IUBACS.BITNET)
is the coordinator of this fine effort. There is also much
software available here for IBM and other systems.
Below is a short description provided by Don Gilbert:
--------------------------------------------------------------------
IUBIO ARCHIVE FOR BIOLOGY
The IuBio Archive will maintain biology software and data. Molecular
biology is the area of concentration. It will include software for
Macintosh, VAX-VMS, Unix, MS-DOS and any other important computer
operating systems. Access to the archive is via anonymous FTP (file
transfer protocol) programs that access computers on the Internet.
ACCESS TO IUBIO ARCHIVE
-----------------------
IuBio is on the Internet network of computers with the name
IuBio.Bio.Indiana.Edu (IP name)
129.79.1.101 (IP address)
If your computer system is linked to the Internet, it probably has an
FTP program. Each FTP program has it's own peculiarities, but most
follow a general syntax:
ftp iubio.bio.indiana.edu -- connect to iubio
user: anonymous
password: guest or your real user name (prefered)
? or help -- general help for ftp
cd [.subdirectory] -- change directory
binary -- use full binary transfer
ascii -- use text transfer
get any.file -- fetch a file from the archive
put my.file -- put a file to the archive
(only for [archive.receive] directory)
bye -- close the connection
CURRENT CONTENTS OF THE ARCHIVE
-------------------------------
An abbreviated directory of the archive is
Directory IUBIO$DUA0:[ARCHIVE]
ARCHIVE.DOC;2 About this archive
ARCHIVE.LIS;1 Full Archive directory list
BIOLOGY.DIR;1 General biology
CHEMISTRY.DIR;1 Chemistry
HELP.DIR;1 Help documents
MOLBIO.DIR;1 Molecular biology
RECEIVE.DIR;1 Place for contributions
SCIENCE.DIR;1 General sciences
UTIL.DIR;1 Computer and archive utilities
Directory IUBIO$DUA0:[ARCHIVE.MOLBIO]
ALIGN.DIR;1 Sequence alignment, including multiple aligners
DATA.DIR;1 Molecular data
EVOLVE.DIR;1 Evolution and phylogeny
IBMPC.DIR;1 MSDOS software
MAC.DIR;1 Macintosh software
RNAFOLD.DIR;1 RNA secondary structure
SEARCH.DIR;1 Databank searching
Most of the software is as received from the authors or other. In the case of
software source, it may or may not be ready to compile and run on a given
operating system.
I plan to be adding more software, data and documentation over the next
several months. If you have suggestions, questions or comments, please
let me know. Addresses are listed below.
CONTRIBUTING TO THE ARCHIVE
---------------------------
Contributions of broad interest in any area of biology, and related
areas of chemistry and other sciences, are welcome. These may be
software or data. Contributions of interest over several computer
platforms should either be plain text files or .ARC archives. You may
put your contribution in the [Archive.Receive] directory, using your FTP
put command. You may also send e-mail compatible files (usually .UUE or
..HQX encoded files or plain text) to
Archive@IUBio.Bio.Indiana.Edu (preferred IP address)
GilbertD@IUBACS (bitnet address)
Don Gilbert, BioComputing Office (land mail)
Biology Department, Indiana University
Bloomington, IN 47405 USA
Any general mail about the archive should be addressed here also.
This archive of biology software and data is sponsored by the Biology
department, Unversity Computing Services, and Institute of Molecular
Biology, at Indiana University and by your hard working archivist, Don
Gilbert.
USING THE ARCHIVE
-----------------
Users not familiar with the Vax VMS operating system of this archive
will find the subdirectory syntax a bit weird. To change from one
directory to another, as from your FTP program, you need to enclose
directory path in square brackets "[]". To change from the main
directory to a subdirectory, use the command:
ftp> cd [.subname]
See Archive.Doc in the archive for further details.
-- Don Gilbert