Staden Information

Staden "R." rs at mrc-lmb.cam.ac.uk
Mon Jan 16 11:49:51 EST 1995


Dear colleague,

Thanks for your enquiry about our software. The package covers most
sequence analysis applications including DNA assembly, DNA analysis,
protein sequence analysis, sequence comparisons, library handling
and searching. Our assembly program can handle input from digitizers,
ABI 373A, LI-COR, Amersham and Pharmacia ALF sequencing machines.

Most of our current efforts are focused on the parts of the package that
deal with sequence assembly and we are supporting, among others, the C. 
elegans sequencing project. More than 10 million bases of finished sequence 
from this project alone have been processed by the package so far.

Our method of dealing with the sequence libraries is unusual in that we
do not reformat them. This saves time and disk space. For each of the 
libraries we create indexes which allow our software to provide instant
searching on entrynames, accession numbers, authors and text. The text
includes all words in the feature tables, not just keywords. EMBL and
SWISSPROT can be read directly from the CDROM using their own indexes.
GenBank and PIR can be used without change once the indexes have been
created. 

We support the software on 

Sun SPARC (SunOS 4.1) eg SPARCstation IPX
Sun SPARC10 (solaris 2.1) eg SPARCstation 10/30
DEC MIPS (Ultrix) eg DECSTATION 5000/240
DEC ALPHA (OSF 1) eg DEC 3000/500
SGI R4000 (IRIX) eg Indigo R4000
Alliant fx2800

We expect it also runs on other UNIX boxes.  Also we have a version
for VAXes and VMS but its development was stopped in April 1991
and its future development is undecided. Those with hardware we
don't support will require ANSI C and FORTRAN77 compilers.  The
programs require either tektronix terminals/emulators, or X
terminals/emulators. The X versions require X11 release 4 or later.
The package is distributed on tape (QIC-150 and exabyte (8mm)).

The package has online help and a 170 page manual which is available
as a Microsoft WORD file on a Macintosh floppy disk, in RTF format
and as postscript.

If you want further information plus application forms, and you
haven't already done so, please send your full postal address.

Recent publications include:

Staden,R Finding protein coding regions in genomic sequences. Methods in
Enzymology 183, 163-180. (1990).

Staden,R Searching for patterns in protein and nucleic acid sequences. 
Methods in Enzymology 183, 193-211. (1990).

Staden,R Screening protein and nucleic acid sequences against libraries of
patterns, DNA Sequence 1, 369-374 (1991).

Dear,S and Staden,R A sequence assembly and editing program for efficient 
management of large projects, Nucleic Acid Res. 19, 3907-3911 (1991).

Staden,R and Dear,S Indexing the sequence libraries: Software providing
a common indexing system for all the standard sequence libraries. DNA
Sequence 3, 99-105 (1992).

Dear,S and Staden,R A standard file format for data from DNA sequencing
instruments. DNA Sequence 3, 107-110 (1992)

Staden,R Software for sequence analysis. Genome News 13, 21-23 (1993)




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