Sentence examples for bits per base from inspiring English sources

To describe our adaptive hash algorithm, first recall that input sequences in Murasaki are stored with two bits per base.

As said, a single genome in its compact encoding (2 bits per base) seems almost incompressible.

A naive representation (2 bits per base, packed), would use 50 bits per 25-mer, or about 26 GB.

Most of these works [ 39, 40, 42, 51] encode one of the genomes in a collection with simple means, spending about 2 bits per base, and then apply very efficient differential LZ-like encoding for the remaining genomes.

The pioneering algorithm of this kind, RLZ [ 42, 52], looks for LZ-matches in the reference genome (the one encoded naïvely, with 2 bits per base), and encodes their positions compactly, with reference to the previous match.

Therefore, a natural way to form a hash key is to compress the k-mer using 2 bits per base, then use it as an offset into a table with an entry for each k-mer (Fig. 1A).

Rather than filtering out possible splice sites with a scoring scheme, TopHat aligns all sites, relying on an efficient 2-bit-per-base encoding and a data layout that effectively uses the cache on modern processors.

It uses two-bits-per-base encoding of the DNA alphabet for both the reference and read sequences.

To achieve compression, it is necessary to represent multiple bases with a single byte, as in the two-bits-per-base schema.

In fact, the average conditional entropy of a base genome given the previous bases is estimated to be closer to 1 bit per base [13] [14].

It follows that the generally accepted maximal information content of 2 bit per base pair only holds true if the two sister strands can be distinguished (which requires extra information).