Alignment summary

NWALKER at JHUHYG.BITNET NWALKER at JHUHYG.BITNET
Tue Jun 22 13:12:21 EST 1993


Here is a summary of the mails sent to me with regard to programs that give
shading on sequence alignments on Macs.
Ive edited the mail messages for clarity.

Nige

(Greetings from Yourclassic Park and the Quadrasaurus Max :-)
======================================================================== 29
From: CSMITH at crcvms.unl.edu
Subject: Re: Seq. Alignments.

        Here are a few you might try. I know of them, but do not have them
up-n'-running (I align sequences using GCG) ... so I may not be much
help on that end.

BOXSHADE ; available by anonymous FTP from BIOMED.BIOLAN,UNI-KOELN.DE

PRETTYBOX ; drop Rick Westerman a message at WESTERM at ACLCB.PURDUE.EDU

                Good Luck
                        Chris
Christopher Smith
Department of Biochemistry
University of Nebraska
Internet: CSMITH at CRCVMS.UNL.EDU
======================================================================== 20
From: QUINN at SALK-SC2.SDSC.EDU
Subject: RE: [Resent-MM Mail]   Seq. Alignments.

Check out Maligned by Steve Clark.  It runs on VMS and is on the IUBIO ftp
server.

Cheers,
Anne Marie
======================================================================== 70
From:       pwoollar@(Peter Woollard x3296) crc.ac.uk
Subject:    Re: Seq. Alignments.

   You may be interested in the ALSCRIPT program.

We use it on Suns running SunOS, I do not know if it
is available on platform you could use.


------------------------------------------------------
 ALSCRIPT - Sequence alignment to PostScript

   Copyright:  University of Oxford (1992)

   Author:  Geoffrey J. Barton
   Laboratory of Molecular Biophysics
   The Rex Richards Building
   South Parks Road
   Oxford OX1 3QU
   UK

   Tel: (+44) 865 275368
   Fax: (+44) 865 510454

   gjb at bioch.ox.ac.uk

REFERENCE:
   Barton, G. J. (1993)
   ALSCRIPT a tool to format multiple sequence alignments
   Protein Engineering, Volume 6, No. 1, pp.37-40.
----------------------------------------------------------

ALSCRIPT takes a multiple sequence alignment in AMPS block-file format
and a set of formatting commands and produces a PostScript file.
CLUSTAL and GCG format multiple alignment files may also be used after
being translated to the correct format.

Although written with the aim of producing figures for journal
submission, ALSCRIPT may be used as a tool for interpreting multiple
sequence alignments.  For example, the boxing, shading and font changing
facilities can be applied to highlight amino acids of a particular type
and thus draw  attention  to clusters of positive or negative charge,
hydrophobics, etc.

Programs:

        alscript   The actual program to create the PostScript file.
        msf2blc    Translates a GCG .MSF file to AMPS format.
        clus2blc   Translates a CLUSTAL PIR format file to AMPS format.


Regards,
        Peter Woollard

------------------------------
Internet: p.woollard at crc.ac.uk
Janet:    p.woollard at uk.ac.crc
------------------------------

======================================================================== 84

Yes, I have a program, DNAdraw, which will do what you want, and quite
a bit more.
The program is not officially released yet, but I hope to do so soon.

Marvin Shapiro:   mbs at helix.nih.gov




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