Vmatch
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Application data |
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| Created by | Stefan Kurtz |
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| Principal bioinformatics method(s) | Read mapping |
| Created at | University of Hamburg |
| Maintained? | Yes |
| Licence | Commercial |
| Operating system(s) | Linux |
Summary: A versatile software tool for efficiently solving large scale sequence matching tasks
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Description
Usually, in a large scale matching problem, extensive portions of the sequences under consideration are static, i.e. they do not change much over time. Therefore it makes sense to preprocess this static data to extract information from it and to store this in a structured manner, allowing efficient searches. Vmatch does exactly this: it preprocesses a set of sequences into an index structure. This is stored as a collection of several files constituting the persistent index. The index efficiently represents all substrings of the preprocessed sequences and, unlike many other sequence comparison tools, allows matching tasks to be solved in time, independent of the size of the index. Different matching tasks require different parts of the index, but only the required parts of the index are accessed during the matching process.
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