 VMatch:
the fastest, most memory-efficient software for comparing whole
genomes:
- Vmatch is NewLink Genetics' state-of-the-art string matching
program for efficiently solving large scale sequence matching
tasks. Vmatch is one of the most versatile tools in the market,
with various file input, match constraints and postprocessing
options.
- Vmatch is based on an efficient implementation of enhanced
suffix arrays, which provide the power of suffix trees with lower
space requirements. The use of persistent indices ensures that,
unlike many other sequence comparison tools, matching tasks can
be solved in time independent of the size of the index.
- In contrast to heuristic tools like BLAST, *all* matches
that meet the user-defined criteria are reported with 100% accuracy.
Vmatch is ideally suited for a variety of sequence matching tasks
such as microarray probe design, finding repeat sequences in
genomes, comparative genomics, EST/cDNA clustering, identifying
vector, plasmid and other contaminants in
draft sequences, SNP mapping, sequence masking etc.
- Vmatch has a fully customizable output format and can
be easily integrated in existing bioinformatics pipelines. Certain
matches can readily be selected by user defined criteria, without
intermediate output and subsequent parsing. Other postprocessing
options like masking, chaining and clustering according to various
criteria are also available.
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