Sequence editor wanted

Don Gilbert gilbertd at sunflower.bio.indiana.edu
Wed Jun 14 13:19:00 EST 1995


I can't provide a complete list of unix-based biosequence
editors, but here are ones I know about

GDE -- XWindows based, for Sun, and probably DEC and SGI
    ftp://rdp.life.uiuc.edu/pub/RDP/programs/Editor_GDE/
    ftp://iubio.bio.indiana.edu/molbio/unix/GDE/
     
MASE -- character based, last updated in 1991
    ftp://mbcrr.harvard.edu/MBCRR-Package/mase*

ae2 -- character based, this version is unsupported I believe
    ftp://rdp.life.uiuc.edu/pub/RDP/programs/Editor_AE2/
    ftp://iubio.bio.indiana.edu/molbio/unix/ae2* (for some mods to ae2)
    
You will also be able to get this soon:
SeqPup -- XWindows (also mac & mswindows), expected to be
  available within 1 month, in flavors for Sun, SGI and DEC unix
  ftp://iubio.bio.indiana.edu/molbio/seqpup/

You may want to try Fristensky Sequence Analysis Package (fsap) in
conjunction with GDE for a fuller program:
  find at fsap ftp://ftp.cc.umanitoba.ca/psgendb/fsap.tar.Z

your requirements are -----
> It must minimally be able to:
>
> - read and write in at least one of the "officially blessed" formats: 
>   (GCG,PIR,fasta,..), and 
> - treat the sequence and annotation separately
>
>It would also be nice if one had the option of choosing between different
>output formats, search for and translate ORFs, complement a DNA sequence,
>oggle between RNA and DNA representations, etc. etc. 

Let me comment only on SeqPup for your needs:
  -- writes & reads all officially blessed formats
  -- does not handle annotation of sequences yet (annotations are discarded)
  -- does translation of sequences to/from protein, but does not find ORFs
  -- complements, does dna<>rna, and several other "standard" sequence
     manipulations
  -- restriction maps, links to external applications for,e.g., contig
     assembly (CAP), multiple sequence alignment (ClustalW),
     phylogeny analyses (DNAML, FastDNAml and other phylip package progs).
  
I think MASE and ae2 are not supported at present, and I can't recall their
feature set.  GDE is widely used on Unix systems.  

I know that the Ribosomal Database Project has had a new multiple 
sequence editor (ALE) in development for the last year or two, that is 
based on an enhanced Gnu EMACs editor.  I don't know when/if this 
will be available to the public.  You might contact them at
rdp at phylo.life.uiuc.edu

-- Don


-- 
-- d.gilbert--biocomputing--indiana u--bloomington--gilbertd at bio.indiana.edu




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