Assembly Sequence

FIGURE 11.6 Sequence assembly using overlapping oligonucleotide probes (see Plate 2 for color version). 

Formation of a broad range of materials with a wide variety of general or specific properties and function (such as proteins and enzymes) through a controlled sequence assembly from a fixed number of feedstock molecules (proteins about 20 different amino acids, five bases for nucleic acids, and two sugar units)... 

Repeat the process starting from bases 2 and 3. Note that the amino acid sequence assembled depends crucially on the starting point or reading frame . Addition of a single nucleobase somewhere in the middle of the sequence alters the code entirely. This is known as a frame shift mutation . Try inserting a C after the ATG start code and repeat the protein assembly. 

Sequence assembly tools The iterative sequence alignment by incorporating the matched consensus sequence from the previous search into the subsequent round of search is called sequence assembly. The available tools are Staden assembler, TIGR assembler, and so on. 

In parallel with NGS technological improvements, many algorithmic advances have been made in de novo sequence assemblers using short-read data (80). In many instances, existing computer resources in the laboratory are enough to perform de novo assemblies. The Escherichia coli genome can be assembled in as little as 15 min using a 64-bit Windows desktop computer with 32 Gb of RAM (81). 

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. 

Peltoia, H., H. Soderlund, and E. Ukkonen. SEQAID A DNA sequence assembling program based on a mathematical model. Nucleic Acids Res. 1984, 12, 307-321. 

Huang, X. An improved sequence assembly program. Genomics 1996, 33, 21-31. 

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