Celera Assembler

We briefly describe computational techniques used in four other sequence assembly programs Celera Assembler [8], GAP4 [34], Phrap [19], and TIGR Assembler [18]. Then we indicate the strengths of each program. 

Celera Assembler Assembly of large genomes www.celera.com... 

Finally attention should be called to the most comprehensive and current treatment of the human genome and its impact in science and medicine, which was the subject of an entire special issue of Science. (The issue contained an interesting 4 Vi x 6 foot chart of the annotation of the Celera human genome assembly [33].)... 

A localized assembly approach was also pursued by Celera. In this approach, consensus sequences of BAC contigs from the Human Genome Project were used to partition the random and synthetic reads into components such that the reads in a component come from a megabase region of the genome. Each component was assembled by the WGS method. The localized assembly approach produced slightly better results than the WGS method. 

The approach taken by the private Celera group is somewhat different. They bypass the use of BAG libraries of long DNA pieces. Instead they break up the entire genome info fragments only 2000 to 10,000 nt long and sequence each of these, in chunks of up to about 700 bases (the resolution limit of the instruments). If we have 3 billion bases to worry about, this means a lot of pieces to sort out and assemble in the proper order (actually, only a portion of those are sorted, but it is still a lot). Powerful computers do the sorting to put the puzzle pieces together. 

Many biological databases (databanks) are embedded with tutorials that make it easy to explore their facilities. There are three sources of biological databases in-house dedicated sources (private and limited for focused projects), databases assembled by companies (mainly fees for services extensive and high-quality but expensive and restrictive such as Celera Genomics and Incyte Genomics), and public databases (such as GenBank, EMBL and DDBJ). An important distinction exists between primary (archival) and secondary (curated) databases. The primary databases represent experimental results with some interpretation (Table 14.11). Their record is the sequence or structure as it was experimentally derived. 

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