SeLOX--a locus of recombination site search tool for the detection and directed evolution of site-specific recombination systems.
Site-specific recombinases have become a resourceful tool for genome engineering, allowing sophisticated in vivo DNA modifications and rearrangements, including the precise removal of integrated retroviruses from host genomes. In a recent study, a mutant form of Cre recombinase has been used to excise the provirus of a specific HIV-1 strain from the human genome. To achieve provirus excision, the Cre recombinase had to be evolved to recombine an asymmetric locus of recombination (lox)-like sequence present in the long terminal repeat (LTR) regions of a HIV-1 strain. One pre-requisite for this type of work is the identification of degenerate lox-like sites in genomic sequences. Given their nature-two inverted repeats flanking a spacer of variable length-existing search tools like BLAST or RepeatMasker perform poorly. To address this lack of available algorithms, we have developed the web-server SeLOX, which can identify degenerate lox-like sites within genomic sequences. SeLOX calculates a position weight matrix based on lox-like sequences, which is used to search genomic sequences. For computational efficiency, we transform sequences into binary space, which allows us to use a bit-wise AND Boolean operator for comparisons. Next to finding lox-like sites for Cre type recombinases in HIV LTR sequences, we have used SeLOX to identify lox-like sites in HIV LTRs for six yeast recombinases. We finally demonstrate the general usefulness of SeLOX in identifying lox-like sequences in large genomes by searching Cre type recombination sites in the entire human genome. SeLOX is freely available at http://selox.mpi-cbg.de/cgi-bin/selox/index.
Surendranath
Vineeth
V
Max Planck Institute for the Molecular Cell Biology and Genetics, Dresden, Germany.
Chusainow
Janet
J
Hauber
Joachim
J
Buchholz
Frank
F
Habermann
Bianca H
BH
D001665:Binding Sites; D019020:Directed Molecular Evolution; D015894:Genome, Human; D023281:Genomics; D016325:HIV Long Terminal Repeat; D006801:Humans; D019426:Integrases / Q000378:metabolism*; D020407:Internet; D055029:Inverted Repeat Sequences; D045522:Recombinases / Q000378:metabolism*; D011995:Recombination, Genetic; D012984:Software
D045522:Recombinases; C045073:Cre recombinase; D019426:Integrases