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Circoletto

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visualising sequence similarity with Circos

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# 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:
<pre>
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
</pre>

Circoletto

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