Finding genes in the C. elegans genome
The ACeDB view shown below shows the kinds of information used to predict genes in the completed genome sequence.
An automated genefinding programme (called GeneFinder) was used to estimate a "buest first pass" gene prediction, using a wide range of data. This was then edited or affirmed by expert annotators, using all information available.
From left to right the columns are:
black line with green box: chromosome representation with position of current viewed segment
yellow box: the sequence segment being viewed
scale in bases
GeneFinder gene models represented as boxes (exons) and introns (brackets)
There are then 3x seven columns of annotation for each (forward, from top to bottom) reading frame:
black lines indicate stop codons
light blue boxes indicate segments with high 'hexexon' scores (good evidence of coding function)
yellow boxes indicate methionines
grey boxed indicate repeat and low-quality regions
brown boxes (several columns) indicate significant similarities detectred by Blast to nucleotide sequences
blue boxes indicate significant similarities detected by Blast to protein sequences
A final column of brackets show splice donor (brackets with finials going down) and acceptor (up) sites, with the quality of the site indicated by the height of the bracket.
