visualising sequence similarity with Circos
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LICENSE
README.md
circoletto.pl
circoletto_html.pl
index.html

README.md

Circoletto

visualising sequence similarity with Circos


server: http://bat.infspire.org/tools/circoletto/
citation: http://www.ncbi.nlm.nih.gov/pubmed/20736339
poster: http://bat.infspire.org/tools/circoletto/circoletto.png
code: we provide the main Perl script, and the server's CGI script and HTML page - you'll need Circos, BLAST, and BioPerl
usage:
before you run Circoletto, be sure to:
- have circos & circos-tools (tested with 0.69-3, http://circos.ca/software/download/tools), BLAST (tested with 2.2.25) in your path, and BioPerl (tested with 1.6.901) installed
- check / edit (in the code) the two paths to circos and circos-tools - if we cannot find them, we'll print a warning and exit
- if you need to increase the max_sequences > 200, you also need to edit max_ideograms in Circos' housekeeping.conf

circoletto.pl
either --query or --q (path to) the queries --database or --db (path to) the database or --blastout or --bl (path to) the BLAST output
other (optional) arguments --out_dir output directory, otherwise pwd --out_name output basename (extension will be added automatically) --best_hit set to show only best hit per query --best_hit_type best hit type, 'entry' to show all HSPs per best hit [default], or 'local' to show single best HSP --w_hits set if you want to show only entries with BLAST hits --z_by depth-order ribbons by 'score' (highest at top) [default] / 'score_rev' / 'alnlen' (longest at top) / 'alnlen_rev' --e_value E-value [default: 1e-10] --gep gap extension penalty, set to >=2 if you need to constrain it e.g. for genomic data [default: -1] --flt set to enable pre-filtering of query sequences --html_out set to provide BLAST HTML output (runs BLAST again...) --no_labels set to switch off labels --out_size set radius of output in pixels, so set to '1000' for a 2000x2000 output [default: 1000] --out_type output type, either 'svg', or 'png' [default] --score2colour score to colour ribbons with, 'bit' for bitscore [default], or 'eval' for E-value, or 'id' for % identity --scoreratio2colour score ratio to use for colouring, 'max' for score/max [default], 'minmax' for (score-min)/(max-min) that should give more colour range esp. for % identity --abscolour use absolute scores for colouring, currently only allowed with % identity --maxB1 max score for blue --maxG2 max score for green --maxO3 max score for orange, then it's red --annotation user provided annotation file, see 'example_annotation.txt' --annocolour colour ribbons by 'query' or 'database' default ideogram colours or annotation (see --annotation), or by 'query_rainbow_(colour|grey)' or 'database_rainbow_(colour|grey)' --invertcolour set to colour ribbons by SEQUENCE (i.e. not ORDER) invertion (or reverse complementarity or plus/minus), normal in black, inverted in lime --hide_orient_lights set to hide orientation lights at edges of ideograms, read from green (=beginning) to red (=end) --ribocolours2allow blue, green, orange, red in a format like this (including parentheses) '(green|orange)' or '(blue)' - histograms are not affected --untangling_off set to turn off ribbon untangling --revcomp_q set to reverse complement query DNA sequences --revcomp_d set to reverse complement database DNA sequences --reverse_qorder set to reverse ORDER of query sequences, may help clarity --reverse_dorder set to reverse ORDER of database sequences, may help clarity --reverse_qorient set to reverse ORIENTATION of query sequences which then need to be read anticlockwisely, may help clarity --reverse_dorient set to reverse ORIENTATION of database sequences which then need to be read anticlockwisely, may help clarity --tblastx run 6-frame tBLASTx for DNA vs DNA --cpus number of CPUs to use with BLAST --max_sequences max sequences to allow --max_ribbons max ribbons to allow