Details

Autor(en) / Beteiligte

• Li, Dequan
• Gao, Wen
• Ling, Charles X.
• Wang, Xiaobiao
• Sun, Ruixiang
• He, Simin

Titel

IndexToolkit: an open source toolbox to index protein databases for high-throughput proteomics

Ist Teil von

• Bioinformatics, 2006-10, Vol.22 (20), p.2572-2573

Ort / Verlag

Oxford: Oxford University Press

Erscheinungsjahr

2006

Quelle

MEDLINE

Beschreibungen/Notizen

• A software package, IndexToolkit, aimed at overcoming the disadvantage of FASTA-format databases for frequent searching, is developed to utilize an indexing strategy to substantially accelerate sequence queries. IndexToolkit includes user-friendly tools and an Application Programming Interface (API) to facilitate indexing, storage and retrieval of protein sequence databases. As open source, it provides a sequence-retrieval developing framework, which is easily extensible for high-speed-request proteomic applications, such as database searching or modification discovering. We applied IndexToolkit to database searching engine pFind to demonstrate its effect. Experimental studies show that IndexToolkit is able to support significantly faster searches of protein database. Availability: The IndexToolkit is free to use under the open source GNU GPL license. The source code and the compiled binary can be freely accessed through the website . In this website, the more detailed information including screenshots and documentations for users and developers is also available. Contact:dqli@jdl.ac.cn