Blast-i2b2: Blast for Biological Sequence Comparison in i2b2 Platform

Abstract

Finding the similarities between biological sequences is an important process to analyze these sequences. The similarity between biological sequences can be determined by using sequence alignment methods. BLAST (Basic Local Alignment Search Tool) is a searching tool, which is designed to perform the sequence alignment process. The current BLAST platform compares a biological sequence with a biological sequences database, lists the similar results, and gives the user the ability to download these results to the local machine without storing those results in a form like data repository or data warehouse, thus lacking reusability and further updates of results. In this paper, we introduce BLAST-i2b2, which implements the BLAST on the i2b2 platform, stores BLAST results, and updates the stored result whenever there are changes in the target biological sequence database. A data warehouse is provided that can be used to efficiently store BLAST-i2b2 results, where it can be used for further analysis and faster updates. In addition, the paper presents the i2b2 (Informatics for Integrating Biology and the Bedside) platform and the update BLAST algorithm. The paper also shows the testing of BLAST-i2b2 performance against three different database sizes. The results show that BLAST-i2b2 update process reduces the BLAST run time to 84% for the small database size, 93% for the medium database size, and 97% for the big database size. The sequence analysis part is not within the scope of this paper and it will be taken into account for the future work.