Apple II software for M13 shotgun DNA sequencing

A direct selection strategy for shotgun cloning and sequencing in the bacteriophage M13

A new cloning strategy is described which utilizes direct selection of recombinants for shotgun sequencing in the filamentous bacteriophage M13. Direct selection is accomplished by insertional inactivation of the M13 gene X protein, a powerful inhibitor of phage-specific DNA synthesis when overproduced. An extra copy of gene X was inserted into the intergenic region of M13 and placed under the ...

A General Coverage Theory for Shotgun DNA Sequencing

The classical theory of shotgun DNA sequencing accounts for neither the placement dependencies that are a fundamental consequence of the forward-reverse sequencing strategy, nor the edge effect that arises for small to moderate-sized genomic targets. These phenomena are relevant to a number of sequencing scenarios, including large-insert BAC and fosmid clones, filtered genomic libraries, and ma...

Gap statistics for whole genome shotgun DNA sequencing projects

MOTIVATION Investigators utilize gap estimates for DNA sequencing projects. Standard theories assume sequences are independently and identically distributed, leading to appreciable under-prediction of gaps. RESULTS Using a statistical scaling factor and data from 20 representative whole genome shotgun projects, we construct regression equations that relate coverage to a normalized gap measure...

Improved method for the production of M13 phage and single-stranded DNA for DNA sequencing.

An improved method is described for the efficient production of M13 phage and M13 single-stranded (ss)DNA in a relatively short time period. Infection of E. coli (F') cells with as few as 5 phage particles can yield 10(12) phage particles/mL in 3 hours if the cells are grown in LB broth or SOB broth supplemented with about 5 mM Mg2+. The method tolerates large variations in the initial multipli...

The universal primers and the shotgun DNA sequencing method.