CRS4 Bioinformatics Laboratory, Science and Technology Park Polaris, Pula, Italy.
PLoS One. 2013 May 7;8(5):e62224. doi: 10.1371/journal.pone.0062224. Print 2013.
BLAST-based similarity searches are commonly used in several applications involving both nucleotide and protein sequences. These applications span from simple tasks such as mapping sequences over a database to more complex procedures as clustering or annotation processes. When the amount of analysed data increases, manual inspection of BLAST results become a tedious procedure. Tools for parsing or filtering BLAST results for different purposes are then required. We describe here PARIGA (http://resources.bioinformatica.crs4.it/pariga/), a server that enables users to perform all-against-all BLAST searches on two sets of sequences selected by the user. Moreover, since it stores the two BLAST output in a python-serialized-objects database, results can be filtered according to several parameters in real-time fashion, without re-running the process and avoiding additional programming efforts. Results can be interrogated by the user using logical operations, for example to retrieve cases where two queries match same targets, or when sequences from the two datasets are reciprocal best hits, or when a query matches a target in multiple regions. The Pariga web server is designed to be a helpful tool for managing the results of sequence similarity searches. The design and implementation of the server renders all operations very fast and easy to use.
基于 BLAST 的相似性搜索在涉及核苷酸和蛋白质序列的几个应用中被广泛使用。这些应用程序的范围从简单的任务，如将序列映射到数据库，到更复杂的过程，如聚类或注释过程。当分析的数据量增加时，手动检查 BLAST 结果成为一个繁琐的过程。然后需要用于解析或过滤 BLAST 结果以满足不同目的的工具。我们在这里描述 PARIGA（http://resources.bioinformatica.crs4.it/pariga/），这是一个服务器，允许用户对用户选择的两组序列执行所有对所有的 BLAST 搜索。此外，由于它将两个 BLAST 输出存储在一个 python 序列化对象数据库中，因此可以根据几个参数实时过滤结果，而无需重新运行该过程，也无需额外的编程工作。用户可以使用逻辑操作来查询结果，例如检索两个查询匹配相同目标的情况，或者当两个数据集的序列是相互最佳匹配时，或者当查询匹配多个区域中的目标时。Pariga 网络服务器旨在成为管理序列相似性搜索结果的有用工具。服务器的设计和实现使得所有操作都非常快速和易于使用。
