amino acid alignments

Vivien Bonazzi vivien at ariel.ucs.unimelb.EDU.AU
Sun Aug 27 21:18:41 EST 1995


In article <ae.28.00108D7D at dna.bio.warwick.ac.uk>,
ae at dna.bio.warwick.ac.uk wrote:

  > Does anyone know of a program that can identify amino acids with similar
  > properties (e.g. charge, hydrophobicity) in a multiple sequence
alignment and
  > then highlight these residues for presentation in a table?
  > Andrew Holmes
  > University of Warwick
  > xw at dna.bio.warwick.ac.uk

Andy Law mentioned SeqVu;
There is a Macintosh program called SeqVu that does what you want (I
believe). Anarchie says that you can get it from :-

<ftp://ftp.sunet.se//pub/molbio/mac/seqvu101.hqx>
<ftp://ftp.bio.indiana.edu//molbio/mac/seqvu101.hqx>
<ftp://sunsite.unc.edu//pub/academic/biology/molbio/mac/seqvu101.hqx>

Its $10 shareware.


Yep, it does pretty much what you want and quite well.
Residues can be coloured and/or boxed.Properties that can be defined are
hydrophobicity, homology, identity and residue characteristics (acidic, basic
uncharged polar, non polar). You can also display some combined properties
ie colour residue chacteristics and box homology. Has some other nice features
Files can be exported in PICT format. Watch out for a few bugs in the
manual... and make sure you import your file in the correct format.

an alternative ftp site (from the originators of the program)

gimr.garvan.unsw.edu.au in the /pub directory.

Vivien



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Vivien Bonazzi      	email vivien at ariel.ucs.unimelb.edu.au

Howard Florey Institue of Experimental Physiology and Medicine

University of Melbourne                     _--_|\
Parkville, Victoria                        /      \
AUSTRALIA                                  \_.--.m/ <--- Melbourne
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