http://plasmidb.cvs.sourceforge.net/viewvc/plasmidb/plasmidb-2/app/views/subunit/show.rhtml?revision=1.3&view=markup

I have however one suggestion, can the colours be adjusted a bit? the thin bright-blue on white background is a bit difficult to read for my bad eyes :-)

Then add this line to your environment.rb file.
‘require bio’

and you are set.
for example you can use a model assuming that the model stores some sequence data as follows

#get an array of sequences given an array of feature ids
#This method will return a fasta formatted file of the sequence data
#The feature model has a name field and a residues field.

def self.send_to_fasta(*accessions)
features = Feature.find(accessions)
@my_fasta = []
features.each do |feature|
name = feature.name
seq = Bio::Sequence.auto(feature.residues.to_s)
@fasta_file = seq.to_fasta(name.to_s, 80)
@my_fasta << @fasta_file
end
return @my_fasta
rescue
puts “wrong names or accession numbers”
end

A real easy example is this method within a model

#returns a bio-sequence length given a sequence string
def self.bioseqlen(seq_value)
bio_seq = Bio::Sequence.auto(seq_value)
residues_count = bio_seq.seq.length
return residues_count
end

It can be called as follows
Model.bioseqlen(sequence_string)

Once i get sometime over the weeekend i will write a more detailed fuctionality