Blixem - display multiple alignments against a reference sequence. Usage: blixem [options] [] [X options] contains the reference sequence in FASTA format. is a GFF v3 file containing alignments and other features. If is ommitted, should contain the reference sequence in FASTA format, below a comment line that reads ##FASTA. Both and can be substituted by "-" for reading from stdin (pipe). If is piped, the first line should contain the sequence name and the second the sequence itself. Options: -t , --display-type= MANDATORY Whether to display sequences in nucleotide or protein mode. Must be one of: N = nucleotide P = protein -a , --alignment-names= Specify a string giving the names of the alignments, e.g. "EST_mouse EST_human" etc. -c , --config-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 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 , --map-coords= 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 , --offset= 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= Default sort mode. Use --help option to see details. --squash-matches Compress the alignment lists on start-up. -s , --start-coord= 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. -y , --styles-file= Read color options from a key-value file. Use --help option to see details. --version Show package version number. -z , --zoom-range= 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 Main font. -font Menu font. FEATURES The prefered file format for 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= argument, where 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 -y or --styles-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. [] = ... can be one of: colours: default colours transcript-cds-colours: used to specify a different colour for CDS sections of transcripts is a semi-colon separated list of fill and line colours of the format: can be in any of the forms accepted by XParseColor; these include name for a colour from rgb.txt, such as DarkSlateGray, or a hex specification such as #305050. Example: colours=normal border #0000af ; selected border #0000af ; normal fill white ; \ selected fill #ffddcc ; transcript-cds-colours=normal border #0000af ; selected border #0000af ; \ normal fill white ; selected fill #ffddcc ; Note that selection colors will be calculated automatically if they are not specified (a darker shade of the default color will be used when the feature is selected). 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 | blixem - 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 Based on original code by Erik Sonnhammer 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 Public License; see http://www.gnu.org/copyleft/gpl.txt