Bases and spaces: resources on the web for accessing the draft human genome

The entire sequence of the human genome is not expected to be finished for some time, and gaps are expected to persist into 2003 [1]. In the meantime, the genome exists in 'draft' form: multiple segments of sequence in which we have high confidence, placed relative to one another by mapping information of lower confidence. Many biologists study particular regions of the genome, such as those involved in positional cloning of disease genes, and this type of work is greatly accelerated by having most of the sequence of the region of interest. The draft human genome now includes this information for most of the genome. Unfortunately, no single resource unites the available human genomic sequences with their locations and their gene content, but by combining the varied resources currently available it is possible to devise strategies that fully exploit the draft genome data. So what resources and information are available so far and where can we find them? Note that the databases and resources mentioned in this article and the corresponding URLs are listed in Table 1As recently as 1996, the entire GenBank (Table 1) database contained around 0.65 Gb of DNA sequence; but the draft human genome sequence alone runs to more than 3.08 Gb. Most of the draft sequence is present in GenBank (Table 1) as unfinished, fragmentary BAC (bacterial artificial chromosome) sequences. These consist of a number of non-overlapping, arbitrarily ordered, fragments, or 'contigs', which have been artificially concatenated to produce a single sequence entry for each BAC. Typically, each contig within a BAC is separated from the next by a large number of bases, labeled 'N'. All unfinished BAC entries are subject to irregular updates until they are finished, and this might alter the number and size of the contigs they contain. The most straightforward web interface for retrieving BAC sequence (and various other types of data) is Entrez (Table 1) at the National Centre for Biotechnology Information