Abstract

The standalone BLAST program is a popular tool to search a DNA sequence against the NCBI database. Since NCBI updates its database every day, the user has to download the latest database before he can run his query. Since the NCBI database is huge (by now more than 100M), the download of the whole database is a time-consuming work. With the continue increase of the NCBI database, this issue will become more significant. The best solution is to re-download the whole database periodically. For each day before the user runs the BLAST program, he has to download the update database, such as month.aa. This update database is smaller than the whole database. He then searches the query on both the whole local database and the update database. The merge of the two query results should be equivalent to the query results on the latest whole database. The BlastMerge program is designed for this purpose. BlastMerge program is the tool that can merge the query results of blastn or blastp program. Originally the idea is from Dr. Clement Lam and Dr. Gregory Butler. The key point of the algorithm used in BlastMerge is to use some data structure to store query results. In this major report we designed the BlastMerge tool with the Object Oriented Methodology, developed BlastMerge tool with C++ language on a UNIX platform, and verified BlastMerge tool by merging the query output of yeast.nt and its update.