104 results about "Sequence assembly" patented technology

Systems, methods, and analytical approaches for short read sequence assembly and for the detection of insertions and deletions (indels) in a reference genome. A method suitable for software implementation is presented in which indels may be readily identified in a computationally efficient manner.

The present invention provides a method for efficiently creating assemblies. The present invention also provides a web-based system for scientists to interact with a computer to implement the method. Further the scientist is able to upload and download information to and from the method to and from a database. The present invention also provides an efficient hardware architecture to implement the method.

Computer implemented methods, and systems performing such methods for processing signal data from analytical operations and systems, and particularly in processing signal data from sequence-by-incorporation processes to identify nucleotide sequences of template nucleic acids and larger nucleic acid molecules, e.g., genomes or fragments thereof. In particularly preferred embodiments, nucleic acid sequences generated by such methods are subjected to de novo assembly and / or consensus sequence determination.

The present invention relates to a method for assembly of nucleic acid sequence data comprising nucleic acid fragment reads into (a) contiguous nucleotide sequence segment(s). The method comprises steps of: (a) obtaining a plurality of nucleic acid sequence data from a plurality of nucleic acid fragment reads; (b) aligning the plurality of nucleic acid sequence data to a reference sequence; (c) detecting one or more gaps or regions of non-assembly, or non-matching with the reference sequence in the alignment output of the step (b); (d) performing de novo sequence assembly of nucleic acid sequence data mapping to the gaps or regions of non-assembly; and (e) combining the alignment output of the step (b) and the assembly output of the step (d) in order to obtain (a) contiguous nucleotide sequence segment(s).The present invention further relates to a method, wherein the detection of gaps or regions of non-assembly is performed by implementing a base quality, coverage, complexity of the surrounding region, or length of mismatch filter or threshold. Also envisaged is the masking out of nucleic acid sequence data relating to known polymorphisms, disease related mutations or modifications, repeats, low map ability regions, CPG islands, or regions with certain biophysical features. In addition, a corresponding program element or computer program for assembly of nucleic the sequence data and a sequence assembly system for transforming the nucleic acid sequence data comprising nucleic acid fragment reads into (a) contiguous nucleotide sequence segment(s) are provided.

A system and method are provided for a query language mapping architecture. In an embodiment, the query language mapping architecture includes an Enterprise Java Bean (EJB) interpreting layer to receive one or more EJB persistence requests and to translate the one or more EJB persistence requests to command sequences. In an embodiment, the query language mapping architecture may also include a Structured Query Language (SQL) assembly layer to receive the command sequences from the EJB interpreting layer and to assemble one or more SQL statements based, at least in part, on the command sequences.