![]() ![]() ![]() The indexing strategy used by the PCR primer analysis program of Jim Kent ( = start, ∼kent/src/) is probably the approach that comes closest to our goals, but it is meant to work with primer pairs and not with independent queries.įor fast performance, the implementation of SSAHA or BLAT keep the index or the hash table in the memory. SSAHA, which creates a database hash table in memory to accelerate search functions and was thus expected to perform reasonably well, is optimized to find longer alignments and fails in practice on most of the criteria set out above. Megablast, a variant of the NCBI BLAST suite that uses a word index to reduce the database search space, and then a greedy algorithm to align only highly conserved regions, can be tweaked to efficiently find exact matches to short sequences (see below), although this was not part of its original design. To our knowledge, no software has yet been designed to precisely match these specifications. Ideally, software for word matching should be able to accomplish the following tasks: (i) search very large databases (≫10 9 nucleotides) efficiently (ii) return accurate and fully exhaustive results for short (14–30 nucleotides) query sequences (iii) scale up gracefully to large collections of queries (10 6 queries) (iv) provide a mechanism for finding single- or multiple-nucleotide mismatches in alignments that are global relative to the query. Applications include probe and PCR primer design, mapping of probe sets to genome features, interpretation of digital gene expression analysis experiments, or individual genome re-sequencing. Such words could be the sequences of individual probes from Affymetrix or other gene chips, PCR primers for the amplification of unique genomic regions (STS ), tags derived from SAGE, or MPSS, experiments, or the raw data from next-generation high-throughput sequencers (using e.g. One of the challenges of the post-genomic era is to be able to identify rapidly, in fully sequenced genomes, transcriptomes, and variants thereof, exact or near-exact matches to short words with a limited number of occurrences. ![]()
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