Pacific Biosciences of California, Inc.

David R Rank

Paul S Peluso

John Lyle

Geoff Otto

Stephen Wilson Turner

Jonas Korlach

Daniel Bernardo Roitman

Thang Pham

Yue Xu

David Kagen Hanzel

Fred C Christians

Insil Park

Sonya Clark

Jeffery Wegener

Arekadiusz Bibillo

Jeffrey Wegener

Ron L Cicero

Geoffrey Alan Otto

Arek Bibillo

Ronald L Cicero

Paul Mitsis

John S Eid

Devon Murphy

Chen-Shan Chin

David Hanzel

David K Hanzel

Compositions that include polymerases with features for improving entry of nucleotide analogues into active site regions and for coordinating with the nucleotide analogues in the active site region are provided. Methods of making the polymerases and of using the polymerases in sequencing and DNA replication and amplification as well as kinetic models of polymerase activity and computer-implemented methods of using the models are also provided.

Polymerases for nucleotide analogue incorporation

Methods of producing substrates having selected active chemical regions by employing elements of the substrates in assisting the localization of active chemical groups in desired regions of the substrate. The methods may include optical, chemical and/or mechanical processes for the deposition, removal, activation and/or deactivation of chemical groups in selected regions of the substrate to provide selective active regions of the substrate.

Articles having localized molecules disposed thereon and methods of producing same

Exemplary embodiments provide methods and systems for diploid genome assembly and haplotype sequence reconstruction. Aspects of the exemplary embodiment include generating a fused assembly graph from reads of both haplotypes, the fused assembly graph including identified primary contigs and associated contigs; generating haplotype-specific assembly graphs using phased reads and haplotype aware overlapping of the phased reads; merging the fused assembly graph and haplotype-specific assembly graphs to generate a merged assembly haplotype graph; removing cross-phasing edges from the merged assembly haplotype graph to generate a final haplotype-resolved assembly graph; and reconstructing haplotype-specific contigs from the final haplotype-resolved assembly graph resulting in haplotype-specific contigs.

De novo diploid genome assembly and haplotype sequence reconstruction

Compositions that include polymerases with features for improving entry of nucleotide analogs into active site regions and for coordinating with the nucleotide analogs in the active site region are provided. Methods of making the polymerases and of using the polymerases in sequencing and DNA replication and amplification as well as kinetic models of polymerase activity and computer-implemented methods of using the models are also provided.

The present invention provides methods, reagents and apparatus for conducting single molecule sequencing in an asynchronous manner. The subject methods and compositions are particularly useful for high throughput and multiplexed sequencing.

Asynchronous sequencing of biological polymers

Active surface coupled polymerases, surfaces that include such polymerases, and methods of making and using surface-attached polymerases are provided.

Active surface coupled polymerases

Preparations, compositions and methods of sequencing nucleic acids are provided. The preparations, methods and compositions employ multiple priming sites on a target nucleic acid and typically utilize single molecule sequencing processes to identify sequence portions of the target which are then assembled to obtain the sequence of the target.

Preparations, compositions, and methods for nucleic acid sequencing

Growing community of inventors

Pacific Grove, CA, United States of America

David R Rank