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Blast2GO Mapping Benchmark Results

Blast2GO mapping step is very time-consuming, if you don't use local Blast2GO database. We performed benchmark test using several Blast2GO databases to find out how fast we can perform Blast2GO mapping with local database.

Blast2GO ver. 2.8 results are here and Blast2GO ver. 3 results are here.

Blast2GO ver. 2.8




Elapsed Time


Public Database

758 sec


Shared DB in USA

313 sec


3 sec


  • Mapping speed with Local Database is 250 times fatser than that with public database.
  • Caution
    Mapping speed with Public Database and Shared Database depend on the location you use Blast2GO (See How fast will mapping be with shared database?).

Blast2GO ver. 3


  • Blast2GO Database Used
         Local Database running on 64-bit Windows 7 (database ver. = Feb 2016), Blast2GO ver. 3.1.3 is used.
         Remote Database hosted by BioBam (database ver. = Sep 2015), Blast2GO ver. 3.2.6 Basic is used.
         Remote Database hosted by BioBam (database ver. = Sep 2015), Blast2GO ver. 3.2.6 Pro is used.
  • 10 Example Sequences come with Blast2GO ver. 2.8



Elapsed Time


51 sec


Remote DB(Basic)

210 sec


Remote DB(Pro)

90 sec


  • Mapping speed with Local DB is almost 4 times fatser than that with Basic. Visit here for using local DB with Blast2GO v.3.1 Basic.
  • Mapping speed with Pro is slower than that with Local DB. There is an advantage of using local DB for Pro users. Visit here for easy-to-setup local DB information.
  • Since access methods to remote mapping DB in v.3.1 and v.3.2 are completely different, it is not possible to use local DB in v.3.2 Basic. However, you can use v.3.1 for mapping/annotation and use v.3.2 for the other tasks, because 1) project file (b2g file) is transferable between v.3.1 and v.3.2, 2) ver. 3.1 and 3.2 can be installed on the same Windows machine at the same time.