Adaptive seeds tame genomic sequence comparison

Adaptive seeds tame genomic sequence comparison.

The main way of analyzing biological sequences is by comparing and aligning them to each other. It remains difficult, however, to compare modern multi-billionbase DNA data sets. The difficulty is caused by the nonuniform (oligo)nucleotide composition of these sequences, rather than their size per se. To solve this problem, we modified the standard seed-and-extend approach (e.g., BLAST) to use a...

Genomic Sequence Comparison

Genomic imprinting: Seeds of conflict

In Greek mythology, Medea betrays her homeland to assist her lover, the adventurer Jason, to obtain the Golden fleece. In exile she bears him two children, but later discovers that Jason plans to marry the King of Corynth’s daughter, so that their future children will become heirs to the throne. Seeking revenge, Medea poisons the bride and slaughters her children, leaving Jason with no chances ...

A Novel Pseudo-Alignment Approach to Fast Genomic Sequence Comparison

Standard methods for sequence analysis and phylogeny reconstruction are based on (multiple) sequence alignments. These methods are known to be accurate but if larger genomic sequences are to be analysed they reach their limits. Consequently, faster but less precise alignment-free methods are increasingly used for genomic sequence analysis. In this work, a novel approach to fast genomic sequence...

Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis.

The 4 202 353 bp genome of the alkaliphilic bacterium Bacillus halodurans C-125 contains 4066 predicted protein coding sequences (CDSs), 2141 (52.7%) of which have functional assignments, 1182 (29%) of which are conserved CDSs with unknown function and 743 (18. 3%) of which have no match to any protein database. Among the total CDSs, 8.8% match sequences of proteins found only in Bacillus subti...