[Bioperl-l] Bio::Graphics HOWTO :: about of the color of graph

[Koichi Minamijima]

Hi.
If it knows, please let me know.

I looked at the web page of "BioGraphics HOWTO."
It was used having edited "Example 4."
	http://bioperl.org/HOWTOs/html/Graphics-HOWTO.html#parsing-
blast

[next unless $hit->significance < 1E-20;] 
of the 38th line was only changed into 
[next unless $hit->significance < 1;].

rscu.fas (ftp://ftp.ncbi.nlm.nih.gov/refseq/cumulative/rscu.fas.Z) 
and "One arrangement file" were used, and blastall was done.
The picture was generated when "Exsample 4." was performed using the 
result.

↓The picture of a result↓
	http://masrao.com/img/render4.png (total)
	 or
	 http://masrao.com/img/render4.jpg (A part)

↓A part of result of BLAST↓
//-------------------------------------------start--------------------
-----------------------//

	>gi|32563818|ref|NP_871912.1| (NM_182112) ROLler: helically 
twisted,animals roll when moving ROL-8, COLlagenstructural gene (rol-8)
 [Caenorhabdtis elegans]
           Length = 265

	  Score = 70.1 bits (170), Expect = 2e-11
	  Identities = 37/95 (38%), Positives = 56/95 (58%), Gaps = 8/
95 (8%)

	Query: 11  
EVGRFRRNAFSAVALSTSCILAIVVLTPIAYQAIQRIHSNLLNDAHFCQARNRDLWTETM 
	70
	            E  + RR AF AV +ST+ ++A VV  P+ Y  +Q   S+L+ +  +C+
AR+RD+W E
	Sbjct: 8   
EQRQMRRIAFVAVVVSTAAVIASVVTLPMLYNYVQSFQSHLMVETDYCKARSRDMWLEMT 
	67
	
	Query: 71  KMARSRGRDEELVARTKRAVKGTWLFGQYIPDRSS 105
	             +   +G       R KRA    WLFGQ+IP+ S+
	Sbjct: 68  ALQAGKGMGH----RMKRA----WLFGQWIPETSA 94



	  Score = 59.7 bits (143), Expect = 3e-08
	  Identities = 24/37 (64%), Positives = 25/37 (67%)

	Query: 291 PGPYGKPGQPGAPGPDGSAGEKGGCDHCPPPRTPPGY 327
	            PG  G+ G  G  GP G  GEKG C HCPPPRTPPGY
	Sbjct: 229 PGHEGRAGPNGPAGPPGDNGEKGDCGHCPPPRTPPGY 265

	 >gi|17533809|ref|NP_496362.1| (NM_063961) COLlagen 
structural gene(29.2 kD) (col-82) [Caenorhabditis elegans]Length = 306

	  Score = 57.8 bits (138), Expect = 1e-07
	  Identities = 23/36 (63%), Positives = 24/36 (66%)

	Query: 292 GPYGKPGQPGAPGPDGSAGEKGGCDHCPPPRTPPGY 327
	            G  G+PG  G  GP G  G  GGCDHCPPPRT PGY
	Sbjct: 271 GAAGQPGAAGEQGPAGEPGAGGGCDHCPPPRTAPGY 306



	  Score = 42.7 bits (99), Expect = 0.004
	  Identities = 20/76 (26%), Positives = 38/76 (50%)

	Query: 10 
LEVGRFRRNAFSAVALSTSCILAIVVLTPIAYQAIQRIHSNLLNDAHFCQARNRDLWTET 
	69
           +E    R+ AF  + +ST   L  +V  P+ Y  +Q + S L  +  FC+ R   L+ +
	Sbjct: 12 
VEAESLRKVAFFGICISTVATLTAIVAIPLLYNYMQHVQSTLQTEVDFCKHRTNGLFDQY 
	71

	Query: 70 MKMARSRGRDEELVAR 85
	            +M + +G   +L+ +
	Sbjct: 72 ERMQQLKGVRGKLIVK 87

//---------------------------------------------------end--------------
-----------------------//

Please compare the portions of 292-327 of NM_182112 and NM_063961.
Graph is white, although NM_182112 are higher as for a score and e-
value is low.

It pats, although it is written to "http://bioperl.org/HOWTOs/html/
Graphics-HOWTO.html#addingscale" as "We specify the base background 
color (-bgcolor => 'blue') and and the minimum and maximum scores to 
scale to. (-min_score and-max_score)", and it is ?
Is it different in HSP?

It is a long text and is pardon. 
Teach, if there are those who understand some.
It is it and English which is hard to read, and is pardon.