High-throughput alignment methods for extension and discovery

Abstract

The invention provides an automated method of simultaneously identifying sequence information extending a plurality of seed sequences. The method consists of: (a) searching a plurality of target sequences with a multiplex query comprising a plurality of seed sequences; (b) identifying a plurality of target sequences substantially aligning with a plurality of seed sequences; (c) selecting a plurality of substantially aligned target sequences containing sequence extending information for a plurality of seed sequences, and (d) repeating steps (a) through (c) using the selected plurality of substantially aligned target sequences as a plurality of seed sequences. Also provided is an automated method of simultaneous identifying a plurality of gene sequences within a plurality of genomic region sequences. The method consists of: (a) pruning nucleic acid sequence elements from a plurality of genomic region sequences to produce a plurality of genomic seed sequences; (b) searching a plurality of target gene sequences with a multiplex query comprising a plurality of genomic seed sequences; (c) identifying a plurality of target gene sequences substantially aligning with a plurality of genomic seed sequences, and (d) locating regions of substantial alignment of the identified plurality of target gene sequences within the plurality of genomic region sequences, the regions of substantial alignment identifying a plurality of gene sequences.

Dependencies are inferred from the claim text.