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.

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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.

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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