BLIXEM(1)

💖 NAME 💖

blixem — bestie, this thing displays multiple alignments against a reference sequence. That's the whole vibe. 🧬✨

🌸 DESCRIPTION 🌸

okay so. Blixem — display multiple alignments against a reference sequence. That's literally what it does, no notes. 💅

Here's how you run it, and yes you have to say it exactly like this:

blixem [options] [<sequence_file>] <data_file> [X options]

so let's talk about those files, because they are the main characters here 🫶

• <sequence_file> holds the reference sequence in FASTA format.
• <data_file> is a GFF v3 file containing alignments and other features.
• if you skip <sequence_file>, then <data_file> should contain the reference sequence in FASTA format, sitting below a comment line that reads ##FASTA.

Both <sequence_file> and <data_file> can be swapped out for "-" to read from stdin (the pipe situation 🥤). And if <sequence_file> is piped, the first line should contain the sequence name and the second the sequence itself. got it? got it. 💜

Now the options, bestie, there are a LOT and I love that for us:

✨ OPTIONS ✨

• -t <type>, --display-type=<type> — MANDATORY 🚨 like actually you cannot skip this one. Whether to display sequences in nucleotide or protein mode. Must be one of: N = nucleotide, P = protein.
• -a <names>, --alignment-names=<names> — give it a string with the names of the alignments, e.g. "EST_mouse EST_human" etc. 🐭🧑
• -c <file>, --config-file=<file> — read configuration options from file.
• --abbrev-title-on — abbreviate window title prefixes ✂️
• --abbrev-title-off — do not abbreviate window title prefixes, leave them long and dramatic
• --compiled — show the package compile date 📅
• -d <data_file>, --data-file=<data_file> — alternative way of specifying <data_file> using an argument
• --dataset — optional string to indicate a data-set that the alignments are from 🗂️
• -e <sequence_file>, --sequence-file=<sequence_file> — alternative way of specifying <sequence_file> using an argument
• --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 the --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 ➡️
• -y <file>, --styles-file=<file> — read color options from a key-value file. Use the --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 🌍

🫶 also, some X options, bestie, so you can be cute about fonts: - -acefont <font> — main font - -font <font> — menu font

👑 THE WHOLE LORE SECTION 👑

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) 2009-2015: Genome Research Ltd. Blixem is distributed under the GNU General Public License; see http://www.gnu.org/copyleft/gpl.txt ⚖️

Version 4.44.1 14:27:56 Oct 19 2017

🦋 AUTHOR 🦋

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. slay. 💜

and that's the whole page, bestie!! this is blixem version 4.44.1, dated October 2017, and it ate, no cap 💅✨🎀