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Command Line Tool
|Usage||Back to top|
$ ruby gene_painter.rb -i <alignment> -p <yaml_files> [<options>]
|-i or --input||Path to fasta-formatted multiple sequence alignment|
|-p or --path||Path to folder containing gene structures in YAML or GFF format|
|Standard output format||Mark exons by '-' and introns by '|'|
|Options||Back to top|
Text-based output format
|--intron-phase||Mark introns by their phase instead of '|'|
|--phylo||Mark exons by '0' and introns by '1'|
|--spaces||Mark exons by space (' ') instead of '-'|
|--no-standard-output||Specify to skip standard output format.|
|--alignment||Output the alignment file with additional lines containing intron phases|
|--fuzzy N||Introns at most N base pairs apart from each other are aligned|
Graphical output format
|--svg||Draw a graphical representation of genes in SVG format.|
|--svg-format FORMAT||Switch between different formats.
FORMAT must be one of "normal", "reduced" or "both"]
"normal" draws details of aligned exons and introns [default]
"reduced" focuses on common introns only
"both" draws both formats
|--pdb FILE||Mark consensus or merged gene structure in pdb FILE
Consenus gene structure contains introns conserved in N % of all genes
Specify N with option --consensus N; [default: 80%]
Two scripts for execution in PyMol are provided:
'color_exons.py' to mark consensus exons
'color_splicesites.py' to mark splice junctions of consensus exons
|--pdb-chain CHAIN||Mark gene structures for chain CHAIN. [default: Use chain A]|
|--pdb-ref-prot PROT||Use protein PROT as reference for alignment with pdb sequence. [default: First protein in alignment]|
|--pdb-ref-prot-struct||Color only intron positions occuring in the reference protein structure.|
|--tree||Generate newick tree file and SVG representation|
Meta information and statistics
|--consensus N||Mark all introns conserved in N % genes. Specify N as decimal number between 0 and 1.|
|--merge||Merge all introns into a single exon intron pattern|
|--statistics||Output additional file with statistics about common introns.
To include information about taxomony, specify options --taxomony and ‑‑taxonomy‑to‑fasta.
|--taxonomy FILE||Use this option to mark introns by taxonomy.
NCBI taxonomy database dump file FILE
OR Excerpt of NCBI taxonomy. Lineage must be semicolon-separated list of taxa from root to species.
|--taxonomy-to-fasta FILE||Text-based file mapping gene structure file names to species names.
One or more genes given as semicolon-separated list and species name.
Delimiter between gene list and species name must be a colon. The species name itself must be enclosed by double quotes like this "SPECIES"
|--taxonomy-common-to X,Y,Z||Mark introns common to taxa X,Y,Z. List must consist of at least one NCBI taxon (scientific name)|
|--[no-]exclusively-in-taxa||Mark introns occuring (not) exclusively in listed taxa.
[default: not exclusively]
|--introns-per-taxon||Mark newly gained introns for every inner node in taxonomy.|
Parse NCBI taxonomy
|--no-grep||Read the NCBI taxomony dump into RAM. This will require some additional hundert MBs of RAM. [default: taxomony dump is parsed with grep calls]|
|--nice||Run grep calls with lower priority. Please make sure to have nice in your executable path when using this option.|
Analysis and output of all or subset of data
|--analyse-all-output-all||Analyse all data and provide full output [default]|
|--analyse-all-output-selection||Analyse all data and provide text-based and graphical output for selection only. All introns are analysed, including those not present in selection|
|‑‑analyse‑selection-output‑selection||Analyse selected data and provide output for selection only|
|‑‑analyse‑selection‑on‑all‑data-output‑selection||Analyse intron positions of selected data in all data and provide output for selection only. Introns present in selection are analysed in all data|
Selection criteria for data and output selection
|--select-all||No selection applied (default)|
|--selection-based-on-regex "REGEX"||Regular expression applied on gene structure file names. Regex must be enclosed by double quotes|
|--selection-based-on-list X,Y,Z||List of gene structures to be used|
|--selection-based-on-species SPECIES||Use all gene structures associated with species. Specify also --taxonomy-to-fasta to map gene structure file names to species names|
|-o or --outfile FILENAME||Prefix of the output files.|
|--path-to-output PATH||Path to the location where output files should be stored.|
|--range START,STOP||Restrict genes to range START-STOP in alignment|
|--[no-]delete-range||(Not) Delete specified range|
|--keep-common-gaps||Keep common gaps in alignment. This option effects only output of --alignment|
|--no-best-position-introns||Plot introns always onto beginning of a gap.
Default: Align introns if their position differs by alignment gaps only
|--[no-]separate-introns-in-textbased-output||(Not) Separate each consecutive pair of introns by an exon placeholder in text-based output formats.
Default: Separate introns unless the output lines get too long.
|-h or --help||List all options available.|
|Changes in command line parameters from v.1.0 to v.2.0||Back to top|
|v.1.0 parameter||v.2.0 parameter|
|-svg WIDTH,HEIGHT FORMAT||--svg and --svg-format|
|-start START and -stop STOP||--range START,STOP|
|-consensus||--consensus, no longer restricted to combination with -pdb|
|-f and -penalize_endgaps||obsolete|