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Blixem - display multiple alignments against a reference sequence.
Usage: blixem [options] [<sequencefile>] <datafile> [X options]
<sequencefile> contains the reference sequence in FASTA format.
<datafile> is a GFF v3 file containing alignments and other features.
If <sequencefile> is omitted, <datafile> should contain the reference
sequence in FASTA format, below a comment line that reads ##FASTA.
Both <sequencefile> and <datafile> can be substituted by "-"
for reading from stdin (pipe). If <sequencefile> is piped, the first
line should contain the sequence name and the second the sequence itself.
Options:
-t <type>, --display-type=<type> MANDATORY
Whether to display sequences in nucleotide or protein mode. Must be one of:
N = nucleotide
P = protein
-a <names>, --alignment-names=<names>
Specify a string giving the names of the alignments, e.g. "EST_mouse EST_human" etc.
-c <file>, --config-file=<file>
Read configuration options from 'file'.
--compiled
Show package compile date.
--dataset
Optional string to indicate a data-set that the alignments are from.
--dotter-first-match
Call Dotter on the first match to the right of the default start coord.
--fetch-server <nodeid:port>
Causes Blixem to get sequences from a fetch server at machine 'nodeid' on the given
port (default 22100).
-h, --help
More detailed usage information.
--hide-big-picture
Hide the big picture section on start-up.
--hide-inactive-strand
Hide the inactive strand (i.e. the reverse strand, or the forward strand if the -R option
is used).
--highlight-diffs
Enable 'highlight differences' mode, where mismatches (rather than matches) are highlighted.
--invert-sort
Invert sorting order
-m <from[:to]>, --map-coords=<from[:to]>
Map the coordinate system so that the given 'from' coordinate maps to the given
'to' coordinate (or to '1' if 'to' is not given).
-n, --negate-coords
When showing the reverse strand, negate the display coordinates.
-o <n>, --offset=<n>
Offset the reference sequence coordinate system by n.
--optional-data
Parse additional data such as organism and tissue-type on start-up.
--remove-input-files
Delete the input files after they have been parsed.
-r, --reverse-strand
Indicates that the given reference sequence is the reverse strand.
--save-temp-files
Save any temporary files created by Blixem.
--show-coverage
Display the coverage section on start-up.
--sort-mode=<mode>
Default sort mode. Use --help option to see details.
--squash-matches
Compress the alignment lists on start-up.
-s <n>, --start-coord=<n>
Start with the display centred on coordinate n.
--start-next-match
Start with the display centred on the first match to the right of the default start coord.
--styles-file=<file>
Read color options from a key-value file. Use --help option to see details.
--version
Show package version number.
-z <start:end>, --zoom-range=<start:end>
Specify the initial range of coordinates to zoom the big picture in to.
--zoom-whole
Start with the big picture zoomed out to view the full reference sequence range.
Some X options:
-acefont <font> Main font.
-font <font> Menu font.
FEATURES
The preferred file format for <datafile> is GFF v3. (However, Blixem is still compatible with
older file formats such as exblx and seqbl, as used by MSPcrunch).
Blixem is mainly aimed at displaying alignments, but can also show other features such as
transcripts, variations and polyA tails. The supported SO terms are:
match
nucleotide_match
protein_match
match_part
match_set
transcript
primary_transcript
processed_transcript
mRNA
CDS
UTR
exon
intron
SNP
copy_number_variation
substitution
insertion
deletion
sequence_alteration
polyA_signal_sequence
polyA_site
read
region
SORT MODE
The sort mode is specified with the --sort-mode=<mode> argument, where <mode> is
one of the following:
s = by Score
i = by Identity
n = by Name
p = by Position
If optional data is loaded on start-up using the --optional-data argument, then the following
sort modes are also valid:
t = by Tissue type
m = by Strain
g = by Gene name
o = by Organism
COLOR KEY FILE
The color key file is specified with the -k <file> or --key-file=<file> argument. This is a .ini-
like file that specifies attributes such as fill and line colors for features from particular
sources (say EST_Human or polya_signal). The file should contain one or more source stanzas followed
by one or more key=value pairs, i.e.
[<source>]
<key>=<value>
...
<value> is a hex color-string, e.g. #ff0000
Possible keys are:
fill_color (default fill color)
fill_color_selected (fill color when selected)
line_color (default line color)
line_color_selected (line color when selected)
fill_color_utr (default fill color for UTR regions)
fill_color_utr_selected (fill color for UTR regions when selected)
line_color_utr (default line color for UTR regions)
line_color_utr_selected (line color for UTR regions when selected)
Only fill_color and line_color are mandatory; the selection colors will be calculated automatically
if not specified (a darker shade of the default color will be used when the feature is selected).
For transcripts, the fill_color/line_color/etc items are used for CDS regions and different colors
can be specified for UTR regions using fill_color_utr, line_color_utr etc.
MSPcrunch
To make the datafile from blast output, run MSPcrunch with option -q.
o To pipe MSPcrunch output directly to Blixem, use "-"
as the second parameter ([datafile]). Example:
MSPcrunch -q <my.blast_output> | blixem <my.seq> -
o The BLAST program (blastp, blastn, blastx, tblastn, tblastx)
is automatically detected from the Blast output header by MSPcrunch
and is passed on to Blixem in the seqbl format (-q).
-----
Written by Gemma Barson <gb10@sanger.ac.uk>
Based on original code by Erik Sonnhammer <Erik.Sonnhammer@sbc.su.se>
Reference: Sonnhammer ELL & Durbin R (1994). A workbench for Large Scale
Sequence Homology Analysis. Comput. Applic. Biosci. 10:301-307.
See http://www.sanger.ac.uk/resources/software/seqtools/ for more info.
Copyright (c) 2009-2011: Genome Research Ltd.
Blixem is distributed under the GNU General Public License; see http://www.gnu.org/copyleft/gpl.txt
Version 4.10-1-g6bff 17:38:25 Apr 4 2012
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