ACeDB
ACeDB
is a database and analysis program initially written for the C. elegans genome
project but now in use for many other genome sequencing projects
worldwide. While the C. elegans genome community is now served by the WormBase database, a web-available database that includes many different kinds of data. However, underneath WormBase, an ACeDB engine still delivers map information.
Start and Stop codons,
splicing...
In the image below, a gene on
C. elegans chromosome
III has been predicted based on the presence of start and stop codons
(yellow boxes and black bars), open reading frames (blue boxes),
splice sites and coding probability. The solid yellow bar with the
scale represents the sequenced DNA. Introns are indicated by > spanning the boxes representing exons.
Defining genes by
similarity to other sequences
In the following panel, another area of chromosome II
is represented. The solid yellow bar with the scale represents the
sequenced DNA. Genes are predicted on both strands. Introns are
indicated by > spanning the boxes representing exons. For the
"down genes" with the ATG at the top of the image, similarities to
other sequences in the databases are shown. The blue rectangles are
similarities between the predicted protein coding content of the DNA
and protein sequences in the databases (determined by BLASTX search)
and the column of yellow boxes represents similarities toC. elegans ESTs
derived from cDNAs (a BLASTN search). The column of turquoise boxes
represent similarity to defined families of repeat sequences inC. elegans, and the
final column on the right, of black bars, represents the presence of
short inverted and direct repeats. The putative identities assigned
to the genes are given to the right.
ACeDB also displays
genetic map
data and physical map
data, and can act as a complete genome
database.
Genetic map
view of C. elegans
chromosome III
Physical
map view of C.
elegans chromosome I central
region
