Sequencing by synthesis based ordered restriction mapping
First Claim
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1. A method for de novo assembly of genomic sequence information comprising the steps of:
- (i) providing genomic DNA isolated from a specific organism;
(ii) generating sequence information from the genomic DNA by clonally isolating and amplifying the genomic DNA to produce a library of single stranded DNA molecules, sequencing the library by a sequencing by synthesis reaction in order to create whole genome shotgun sequence information, and assembling contigs from the sequence reads obtained from the whole genome shotgun sequence information;
(iii) obtaining whole genome optical restriction map information for the organism'"'"'s genomic DNA for at least one restriction enzyme and generating an ordered restriction map; and
(iv) aligning the sequence information obtained from step (ii) such that the sequence contigs are orientated and ordered with respect to the ordered restriction map obtained in step (iii).
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Abstract
The present invention is directed to a method for de novo assembly of genomic sequence information comprising the combination optical whole genome restriction mapping and ultra high throughput pyrosequencing.
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Citations
8 Claims
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1. A method for de novo assembly of genomic sequence information comprising the steps of:
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(i) providing genomic DNA isolated from a specific organism;
(ii) generating sequence information from the genomic DNA by clonally isolating and amplifying the genomic DNA to produce a library of single stranded DNA molecules, sequencing the library by a sequencing by synthesis reaction in order to create whole genome shotgun sequence information, and assembling contigs from the sequence reads obtained from the whole genome shotgun sequence information;
(iii) obtaining whole genome optical restriction map information for the organism'"'"'s genomic DNA for at least one restriction enzyme and generating an ordered restriction map; and
(iv) aligning the sequence information obtained from step (ii) such that the sequence contigs are orientated and ordered with respect to the ordered restriction map obtained in step (iii). - View Dependent Claims (2, 3, 4, 5, 6, 8)
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7. A computer program product comprising a software program to compare and/or align a whole genome ordered restriction map with multiple contigs obtained from a sequencing by synthesis reaction.
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