Stephen Klautky notes that epd29.seq won't work with the GCG package. This
isn't surprising as those sequences are in FASTA format not GCG format. In
order to use these sequences under GCG one must first convert all of them to
GCG format. Is there a way to do this ? YES! Don Gibert's program
READSEQ converts among a variety of types of sequence formats (kudoes to Don),
including fasta and gcg. I have included a listing of sites where you can get
readseq. Once you have imported readseq, and installed it you can convert the
EPD database with the following command:
readseq -a -f5 epd29.seq | cat > epd29.gcg
Filtering it through cat is important as otherwise it will output each sequence
into a seperate file. This assumes that you are using unix.
OR I could make this (or other sequence formats) file available for ftp if
the authors of epd don't mind. Let me know what you'd like.
Hope this helps,
Dan Jacobson
danj at jhuhyg.sph.jhu.edu
============================================================================
Host anagram.mcs.anl.gov
Location: /pub/RDP
FILE -r-xr-xr-x 4424 Dec 16 15:25 readseq.readme
FILE -r-xr-xr-x 108828 Dec 16 15:25 readseq.shar
Host biom3.univ-lyon1.fr
Location: /pub/bio
FILE -rw-r--r-- 50291 Feb 28 1991 readseq.tar.Z
Host evolution.bchs.uh.edu
Location: /pub/gene-server/mac
FILE -rw-r--r-- 65422 Sep 16 18:08 readseq.hqx
Location: /pub/gene-server/vms
FILE -rw-r--r-- 95733 Sep 16 18:21 readseq.uue
Host fly.bio.indiana.edu
Location: /molbio
DIRECTORY drwxr-xr-x 512 Nov 14 05:30 readseq
Location: /molbio/readseq/iris-bin
FILE -rwxr-xr-x 102664 Nov 14 05:24 readseq.iris
Location: /molbio/readseq/mac-bin
FILE -rw-r--r-- 72408 Nov 14 05:41 readseq.hqx
Location: /molbio/readseq
FILE -rw-r--r-- 108825 Nov 14 05:25 readseq.shar
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FILE -rwxr-xr-x 49152 Nov 14 05:25 readseq.sparc
Location: /molbio/readseq/src
FILE -rw-r--r-- 17488 Nov 14 05:26 readseq.c
FILE -rw-r--r-- 737 Nov 14 05:26 readseqsiow.make
FILE -rw-r--r-- 23102 Nov 14 05:26 ureadseq.c
FILE -rw-r--r-- 2281 Nov 14 05:26 ureadseq.h
Location: /molbio/readseq/vms-vax-bin
FILE -rw-r--r-- 78848 Nov 14 04:50 readseq-vms.exe
FILE -rw-r--r-- 8417 Nov 14 04:50 readseq-vms.obj
FILE -rw-r--r-- 12000 Nov 14 04:50 ureadseq-vms.obj
Host nic.funet.fi
Location: /pub/sci/molbio/vax
FILE -rw-r--r-- 54403 Jan 7 19:50 readseq.zoo
