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This section describes to use sequences which are already available in the GCG environment. WPI users might refer to the WPI chapter for details on how to use sequences in this envoronment. If you want to use sequences which are known in the sequence databases, you do not need to copy these data into your directory but rather use the name of the entry directly - use the local database section for reference.
If you start the 'seqed' program on an existing file, you will end
up directly on the command
line. You may go to the command line
with a special key combination as depicted below, and
you may
finally exit the program by typing
exit.
The following Figure symbolises the screen of the sequence editing
program on the left side,
and the commands required to move from
one level to the next are indicated with arrows.
The program 'seqed' is started by typing its name:
% seqed
You then will be prompted for the name of the sequence you
want to
modify. Do this by responding to the question
seqed
screen mode commands are:
<CTRL><D>
seqed command line mode commands
are:
Another small 'seqed' exercise:
Use the 'seqed' program to create a DNA sequence fragment.
Use the sequence editor 'seqed' and view
the DNA sequence with the
accession number M19311. (You need to give
the name as GENEMBL:M19311.)
You shall extract the
reading frame
of
this sequence - the start and stop codon can be found
in the
annotation
of this sequence - you will want to seek the
CDS
(coding sequence) features, to find the desired codons there.
Name the newly created sequence "my2.seq"
- we will
need this sequence in later exercises.
================================= End Exercise 3
: :
: (Heading area) :
: : ^ |
: : | |
| heading <RETURN> | <CTRL><D>
| v
AGCGCTGACAGCTGAGA |
....|....:....|....:.. | ^ |
(sequence line) | | <RETURN> | <CTRL><D>
| | v
:
(command line) ^ |
| seqed | exit
| v
% (system prompt)
Subsection 7.3.2 Start of the 'seqed' Program
what file?
You are now on the sequence line, this mode is the so-called
screen mode.
Subsection 7.3.3 Screen Mode Commands
Symbol meaning action
------------------------------------------------------------------
1 (number) jump to specified position
-> <- (arrows) move 1 left or right
> < (larger/smaller) move 50 left or right
10 -> (number+cursor) move number left or right
/atg (slash followed by pattern) jump to pattern
You might use <CTRL><R> (if screen weird) to refresh
the screen.
In order to leave
the screen mode, type
Subsection 7.3.4 Command Line Mode Commands
command (example) command (general) action
----------------------------------------------------------------------------
help help on-line help
1,200 Write test.seq n,m write <file> write sequence (fragment) to file
300 Include test.seq n include <file> include new sequence (at pos. 300)
exit exit save work and exit
quit quit cancel work and exit
================================= Begin Exercise 3
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