BLAST -> MSPcrunch -> Blixem
Note that MSPcrunch can also produce output in a format suitable for ACEDB. ACEDB can then later call Blixem with this stored data.
See the file '=README' in the FTP distribution for instructions on installing Blixem and MSPcrunch. Both programs are available in the same FTP directory.
On the command line, you can run MSPcrunch and Blixem in one go by typing:
The yellow sequence is the translated genomic sequence in three
frames for the current orientation. Residues in a homologous protein
may get three different colours: Cyan (bright blue) for the same
residue, dark blue for a conserved substitution and no color of a
mismatch. The Start and End coordinates refer to the entire match,
not just what is displayed at the time. Scrolling is either done with
the scroll buttons, or with the middle mouse button, which also tells
the coordinate of the residue under the crosshair.
Switch to the opposite strand by clicking on "Strand v^".
The button "Goto..." can either be used by picking, to go to an absolute position, or as a pull-down menu with the right mouse button to go to the beginning or end of the query sequence currently in Blixem. When Blixem is called from ACEDB, this is a 40 Kb region around the match that was used to call Blixem.
Quit Exit program. Help Get brief help. Print Print the currently displayed window. Print whole alignment Print all matches. May produce many pages. Change Settings Start the Settings tool. Dotter Do a dotter dotplot with last picked matching sequence. Dotter HSPs only Display blast matches in a Dotter dotplot. Dotter query vs. itself itself. Call Dotter for a region of the query vs. This is useful to analyse internal repeats etc. Manual Dotter parameters Use if Dotter estimates the start and end coordinates wrongly. Automatic Dotter parameters To cancel the Manual mode. Highlight sequences by name Define a template, e.g. *human, to highlight all human proteins. This works on the name field in the leftmost column. Note that the names start with a database prefix that is hidden in blixem, so it's a good idea to always start your template with the wildcard *. Clear highlighted sequences Reset all picked and highlighted sequences.
Sort by score Sort all proteins with the highest-scoring first. Sort by identity Sort all proteins with the most identical first. Sort by name Sort all proteins alphabetically. Sort by position Sort all proteins with the most N-terminal first. Big Picture Toggle Big Picture (top display) on/off. Big Picture Other Strand Toggle between single and double strand display in the Big Picture. Highlight differences Shows identical residues as a dot (.) and draws mismatching residues in bright blue. Squash matches Forces all matches to one sequence onto one line. The start of a match is marked by a red vertical bar. SEG low complexity analysis Draws plots of low complexity at 3 different window sizes. These window sizes by default correspond to SEG's (Wooton) Stringent, Medium and Non-globular levels of low complexity. Print colours Good for printing on black/white printers. No colours Good if you want to colour printout it by hand. Verbose mode Toggles verbose mode and prints all HSPs to stdout.(The Settings tool also allows other settings to be changed, such as colours and efetch method.)
blixem seq foo &
Sonnhammer, ELL and Durbin, R (1994). "An expert system for processing sequence homology data". ISMB 2:363-368