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:[x,y] Get [filename]
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adds the sequence in the
specified file to the group
at column x in row
y. The screen is
erased
and you are prompted to
enter the range and strand.
Unlike the Write and
EXit commands,
Get does not assume any
file extension. You must
type the file name plus
any extension it
requires.
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:[x,y] New [SeqName]
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adds an empty sequence at
column x in row y.
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:[x,y] MOve [SeqName]
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moves the sequence to start
at column x in row
y. If the SeqName
parameter is omitted, the
sequence at the current cursor
position is moved.
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:REMove [SeqName]
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deletes the entire sequence from
the group. If the
SeqName parameter is omitted, the
sequence
at the current cursor position
is removed.
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:REName [OldName] [NewName]
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changes the name of the
sequence. If no names
are provided in the command,
the sequence at
the current cursor position is
renamed and you are prompted
for the new name.
If only one
name is provided, it is
assumed to be the old
name and you are prompted
for the new name.
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:REDraw
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redraws your terminal screen.
This is useful if noise
in the line between your
terminal and the
computer has changed the screen
in some unreasonable way or
if a system message appears
on
your screen.
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:[s] HEAding [SeqName]
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enters Heading Mode to let
you view and edit the
documentary heading. You can
modify any
part of the heading.
Heading Mode is terminated with
<Ctrl>D. The optional SeqName
parameter specifies which sequence heading
you want to edit.
If omitted, the sequence at
the
current cursor position is assumed.
The optional numeric parameter
specifies which line of the
heading you want to start
editing.
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:screen
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returns your session to Screen
Mode. Just pressing <Return>
also returns you to Screen
Mode. (If you prefer
to return to Screen Mode
after every command is executed,
use the
command-line parameter -SINGlecommand.)
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:NUCleotide
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sets the sequence type for
each sequence in the sequence
group to be nucleotide.
This enables
the nucleic acid ambiguity meanings
of the GCG sequence symbols
in pattern searches (with /)
and consensus definition (set the
topic THE CONSENSUS SEQUENCE below).
Also, LineUp
treats nucleic acid sequences as
circular when searching for a
pattern. When the sequences
are
saved to files with either
the Write or EXit command,
they are written as nucleotide
sequences if their sequence type
is nucleotide.
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:PROtein
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sets the sequence type for
each sequence in the sequence
group to be protein.
This forces LineUp
to treat all sequences as
linear in pattern searches and
does not interpret any sequence
characters as nucleotide ambiguity symbols
in pattern searches and consensus
definition (see the
topic THE CONSENSUS SEQUENCE below).
When the sequences are
saved to files with either
the Write or EXit command,
they are written as protein
sequences if their sequence type
is
protein.
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:SPacewalk
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enters Spacewalk Mode, which allows
you to move the cursor
anywhere on the surface to
select a
position for a new sequence.
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:NOSPacewalk
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tells LineUp not to use
Spacewalk Mode but to prompt
for numerical surface coordinates.
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:FOSN
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tells LineUp to use the
list file format when loading
or storing the sequence group.
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:MSF
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tells LineUp to use the
multiple sequence format (MSF) file
when loading or storing the
sequence
group.
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:[s,f] PRint [filename]
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writes a file of the
formatted sequence group from position
s to f. The
format resembles that of
Pretty.
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:SUMmary [filename]
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writes a list of the
names and beginning positions of
the sequences loaded into the
LineUp editor.
This list can go either
to a file or to
your screen (by typing Term
for filename).
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:[n] SLide
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shifts all the sequence starting
positions by n. The
coordinate ruler appears to slide
under the
sequences. n can be
either a positive or negative
number to shift the sequences
to the right or
left, respectively.
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:[s,f] ROWMove [n]
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moves a clump of rows
up or down. The
sequences on rows numbered from
s to f are moved
up
n rows. Negative values
of n move the sequences
down n rows. This
command can be used to
open a row in the
middle of the surface for
another sequence. LineUp will
not let you move
sequences onto rows containing other
sequences not simultaneously being moved.
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:GOto [SeqName]
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moves the cursor to the
beginning of the named sequence.
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:[s,f] CONsensus
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calculates the consensus sequence between
positions s and f.
If the optional positions are
omitted, the entire consensus is
calculated. This command only
works when LineUp is not
in the
Auto Consensus state. (See
the topic THE CONSENSUS SEQUENCE
below for further details.)
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:AUtoconsensus
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makes LineUp recalculate the consensus
sequence each time there is
a change in any of
the
other sequences. When LineUp
is in the Auto Consensus
state, the consensus is strictly
a
function of the other sequences
and cannot be changed directly.
When the sequence group
is
large, recomputing the consensus uses
a lot of machine time
and makes LineUp appear sluggish.
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:NOAUtoconsensus
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turns off the Auto Consensus
state. This allows you
to change the consensus directly.
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:ZIp [filename]
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aligns a new sequence to
the current consensus.
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:Write [filename]
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records the current surface configuration
in a list file and
saves the current version of
each
sequence in a file if
the program is in FOSN
mode (see the FILE NAME
CONVENTIONS topic
below). If the program
is in MSF mode, a
multiple sequence format (MSF) file
is written. If the
filename parameter is omitted, LineUp
uses the sequence group name
specified when the
program is initially run.
If you specify a file
in another directory, all files
are created there.
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:EXit [filename]
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works like the Write command
but stops the session after
writing out the sequences.
The
filename parameter behaves as in
the Write command.
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:Quit
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terminates a session with LineUp
without saving any changes you've
made since the last time
you used the Write command.
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:Help
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shows the commands available in
Screen and Command Modes of
LineUp.
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Heading Mode allows you to
view and edit the documentation
that precedes the sequence in
the
sequence file. All headings
are lost if you write
the sequences into a multiple
sequence format (MSF)
file.
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Entering Heading Mode
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To enter Heading Mode, use
the HEAding command.
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Leaving Heading Mode
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Use <Ctrl>D to return to
Command Mode.
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Moving the Cursor
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You can move around using
the arrow keys. Although
the editing window is only
twenty lines
long, it scrolls over the
heading vertically to let you
see and modify any part.
<Ctrl>E
positions the cursor at the
end of the current line.
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Editing in Heading Mode
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Like many text editors, typing
inserts text at the cursor
and the <Delete> key and
<Ctrl>H delete characters to the
left of the cursor.
<Ctrl>U deletes everything from
the current cursor position to
the start of the line.
Pressing <Return> creates a
new line
starting at the current position
in the heading.
Unlike many text editors, before
letting you edit the heading
LineUp asks you if you
need more
storage. You must enter
the maximum number of lines
that you expect to have
to add. If you
are in Heading Mode and
find you do not have
enough storage for your changes
and additions,
you can exit Heading Mode
and enter it again, specifying
some larger number of lines
for
increased storage.
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LineUp behaves differently depending on
whether you are working with
a protein or nucleotide
sequence group.
If you are working with
a nucleotide sequence group, then
pattern searches (see "Finding Patterns"
under the SCREEN MODE topic)
and the consensus definition (see
the topic THE CONSENSUS
SEQUENCE) assume the IUB nucleotide
ambiguity meanings for the GCG
sequence symbols. Also,
LineUp treats nucleic acid sequences
as circular when searching for
patterns. When the sequences
are
saved to files with either
the Write or EXit command,
they are written as nucleotide
sequences if
their sequence type is nucleotide.
If you are working with
a protein sequence group, then
LineUp treats all sequences as
linear in pattern
searches and does not interpret
any sequence characters as nucleotide
ambiguity symbols in pattern
searches and the consensus definition.
When the sequences are
saved to files with either
the Write or
EXit command, they are written
as protein sequences if their
sequence type is protein.
By default, if the first
sequence entered into the LineUp
editor screen is from an
existing sequence file,
then the type of that
sequence determines the type for
the entire group. If
the first sequence in a
sequence group is entered interactively
from the keyboard, then LineUp
sets the sequence type for
the
entire sequence group to be
protein, by default. LineUp
indicates the type of the
sequence group
(protein or nucleotide) in the
upper-right corner of the editor
screen.
You can specify the sequence
type for the entire group
from the command line with
the -PROtein and
-NUCleotide command-line parameters. Once
you are viewing the editor
screen, you can change the
sequence type for the entire
sequence group with the PROtein
and NUCleotide command mode
commands.
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An optional consensus sequence can
be generated as a function
of the rest of the
sequences in a
sequence group, or, like any
other sequence, typed in by
you.
By default, new sequence groups
contain an empty consensus at
row 0 unless LineUp is
run with the
-NOCONsensus command-line parameter.
If the sequence group has
no consensus, you can create
one using the New command
and giving the
new sequence the same name
as the sequence group.
The CONsensus command and the
AUtoconsensus commands now work on
the row you have designated
for the consensus with the
New
command.
When a consensus sequence is
generated by LineUp, either by
issuing the CONsensus command or
AUtoconsensus command, each consensus character
in the consensus sequence is
replaced with a
character that is a function
of the other characters in
its column. If all
the characters in the column
are
the same letter and at
least one of them is
uppercase, the consensus character is
the uppercase
equivalent of that letter.
If there is more than
one letter in the column,
but one occurs more frequently
than any other, or if
all letters are the same,
but none are uppercase, then
the consensus character is
the lowercase of that letter.
Otherwise, the consensus character
is a dot (.).
The consensus definition also depends
on whether LineUp is working
with a nucleotide or protein
sequence group. If a
protein sequence group is loaded
into the multiple sequence editor,
the above
description is complete. If
a nucleotide sequence group is
loaded into the editor, the
ambiguity codes
are ignored for the purpose
of consensus definition. This
treats all ambiguity codes as
though they
were the code 'N.' LineUp
indicates the type of the
sequence group (protein or nucleotide)
in the
upper-right corner of the editor
screen.
The consensus sequence is distinguished
by having the same name
as the sequence group.
If you
rename the consensus sequence with
the REName command, the name
of the sequence group changes
as well. (You can
rename the group even if
you have no consensus sequence.)
Conversely, if you specify
a file name in a
Write or EXit command, this
changes the name for the
sequence group being saved
and also changes the consensus
sequence name.
The consensus sequence is unique
in that, because it will
likely extend to all columns
determined by
the other sequences, no other
sequence may share its row.
You can delete the
consensus sequence from
your group, and you can
later create a new consensus
sequence. However, an existing
sequence cannot
become the consensus sequence, either
through the REName or Get
commands.
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If you use LineUp with
sequence groups that have different
sequences starting at several different
columns, a problem will arise
when you make deletions or
insertions to whole columns.
For example,
suppose you are assembling a
group of sequences with LineUp.
When a new sequence
is added, you
may decide a previous sequence
reading was incorrect. You
may decide to delete a
base from an old
sequence near the left end
of the assembly. The
tail of that sequence slides
left one column, destroying
its alignment with any sequence
starting to the right of
the deletion site.
The general problem is that
insertions or deletions cause shifts
of register between sequences.
Those
sequences that overlap with the
changed column appear to need
adjustment. But those sequences
that
start down to the right
do not appear misaligned.
LineUp warns you of potential
alignment problems by producing a
warning sign at the top
of the
screen. The sign says
either PUSH-OVER WARNING or PULL-OVER
WARNING, depending on whether
there was an insertion or
deletion. The warning is
only displayed if there are
other sequences that
start to the right of
your change. To make
it easy for you to
correct the alignment problem, LineUp
provides you with screen mode
commands to PULLOVER the sequences
starting to the right of
the
cursor (<Ctrl>P for deletion), or
to PUSHOVER (<Ctrl>I for insertion).
You must make the
decision whether the deletion or
insertion requires adjustments and then
ensure that the adjustments
are correct. It is
not recommended that you blindly
trust the warning sign but
that you let it remind
you of the issue.
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By default, LineUp reads and
writes individual sequence files, grouped
in a list file (FOSN
format).
Using the command-line parameter -MSF
causes LineUp to expect a
multiple sequence format (MSF)
file when reading a sequence
group, and to write out
an MSF file when storing
a sequence group (MSF
format). For instance, the
command % lineup -MSF hsp70 reads the sequences
in the file
hsp70.msf into the LineUp editor
and names the sequence group
hsp70. (See Chapter 2,
Using
Sequence Files and Databases in
the User's Guide for a
complete description of MSF files.)
When
LineUp writes an MSF file,
leading gap characters (.) are
added to those sequences that
do not start at
the beginning of the alignment
so that all sequences are
left-justified in the output file.
The current sequence group format
is indicated as either FOSN:
or MSF: on the top
line of the screen
editor. You can toggle
between these two formats using
the FOSN and MSF commands
in command
mode.
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There is no harm in
using SeqEd to change a
sequence file that has been
written by LineUp. Provided
the name is the same,
the new version is accepted
by LineUp. The only
restriction on replacing
members of a sequence group
is that the new members
must not overlap with other
sequences on the
same row. The information
where the sequence starts is
stored in the list file,
so changing the
sequence file can only change
the length of the sequence.
You can change where
a sequence starts on
the surface by modifying the
Offset and Row columns of
its entry in the list
file using a text editor.
If
you overlap two sequences on
the same row, LineUp refuses
to load one of the
overlapping sequences.
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LineUp does not handle embedded
comments. LineUp can read
files containing embedded comments,
but the comments are lost
and will not appear in
any file written by LineUp.
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If your sequences all start
at the same column, you
can use Pretty to generate
a consensus sequence for
a sequence group created by
LineUp. Pretty uses a
more sophisticated algorithm than LineUp
to
generate a consensus sequence and
you have more control over
the consensus calculation. However,
Pretty can only handle sequence
groups whose left ends are
aligned.
Pretty and LineUp both know
how to read the other's
files of sequence names, so
you can use Pretty to
get a consensus sequence in
Pretty format. Then, % pretty -UGLy
makes a file of sequence
names
that LineUp can read.
However, the consensus sequence defined
by Pretty will not be
recognized as the
consensus sequence of LineUp.
It is named Consensus by
Pretty, whereas LineUp names its
consensus
sequence with the sequence group
name. This is reasonable,
since LineUp will not define
the
consensus in the same way,
so the names should be
different.
If you alternate between using
Pretty and LineUp on a
sequence group having a LineUp
consensus
sequence, you have to preserve
the old sequence group name
when doing Pretty -UGLy in
order to
make LineUp recognize the consensus
sequence. If you give
a new name to the
group, the consensus
sequence is no longer recognizable,
as such, by LineUp.
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Several indicators for LineUp are
displayed on the top row
of the screen. The
left-most word indicates
the name of the sequence
on which the cursor currently
rests. Next, the cursor's
position on the surface
is displayed. Then the
display shows whether LineUp calculates
the consensus automatically every
time you add or delete
a character. The sequence
group name is next, preceded
by either FOSN or
MSF, indicating the file format
to be used for reading
and writing the sequence group.
Finally, LineUp
indicates whether the type of
the sequence group is nucleotide
or protein.
LineUp frequently displays the PULL-OVER WARNING
sign (see the PULL-OVER AND
PUSH-OVER
topic above).
The screen provides a window
onto the sequence surface.
Through this window, 16 of
the 31 surface
rows can be viewed at
one time. As you
move your cursor near the
top row of the window,
for example,
if there are occupied surface
rows past the top of
the window the surface is
scrolled down, letting you
see more lines at the
top of the window and
fewer at the bottom.
When there are more rows
in use than can be
displayed at once, some rows
are hidden above or below
the window. When this
happens a '+' is displayed
next to the top or
bottom row number indicating
hidden rows in that direction.
Although the window also scrolls
horizontally, there is no analogous
sign indicating that you cannot
see
the whole length of the
surface.
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When you save a sequence
group using FOSN format, the
name given to the FOSN
is made up of the
sequence group name followed by
the extension .fil. The
sequence file names are the
sequence names
used in LineUp and the
file extension .frg. When
you save a sequence group
using MSF format, the
name given to the MSF
file is made up of
the sequence group name followed
by the extension .msf.
These file name extensions are
the defaults for LineUp, but
you can specify your own
by using the
command-line parameters -FOSNEXtension, -FRAGEXtension, and
-MSFEXtension (see below).
You can override these choices
when you specify an output
file name; if you include
a file extension, it is
used in lieu of that
given on the command line
or the default.
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The current version of LineUp
cannot recover from a system
crash. If you are
disconnected from
LineUp, you lose everything you
have done since the last
time you saved the group
using the Write or
EXit commands. Therefore, we
recommend that you save your
work frequently using the Write
command so that little is
lost in the event of
a crash.
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There is a Finite Amount
of Storage Space
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LineUp has a total of
one million bytes of storage
for sequences and their headings.
While this is
large, it is finite.
If your sequence group exceeds
this limit, the parameter MEMSIZE
can be
changed in the the file
GenInclude:mem.inc and LineUp can be
recompiled and linked. If
you
make MEMSIZE larger, you may
notice that the computer is
doing a huge number of
page
swaps, making the program needlessly
expensive and inefficient to run.
If you suspect this
is
happening, you should discuss the
possibility of raising the size
of your working set with
your
system manager. This will
reduce the number of page
swaps required.
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LineUp was designed and implemented
by Dr. William Winsborough. We
are very grateful for the
collaboration of Drs. William Boorstein and
Lynn Manseau of the UW
Department of Physiological
Chemistry.
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All parameters for this program
may be put on the
command line. Use the
parameter -CHEck to see
the summary below and to
have a chance to add
things to the command line
before the program
executes. In the summary
below, the capitalized letters in
the parameter names are the
letters that
you must type in order
to use the parameter.
Square brackets ([ and ])
enclose parameter values that
are optional. For more
information, see "Using Program Parameters"
in Chapter 3, Using Programs
in
the User's Guide.
