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Table 4 Details of Speed options in RISCI

From: RISCI - Repeat Induced Sequence Changes Identifier: a comprehensive, comparative genomics-based, in silico subtractive hybridization pipeline to identify repeat induced sequence changes in closely related genomes

Parameters Fast Medium Slow
Blast -v 2 3 5
Maximum no of Blast HSPs compared 100 (in each orientation) 500 (in each orientation) 10000 (in each orientation)
Pros and cons fastest, least accurate Fast, reasonably accurate Most accurate
  1. For each of the speed options (Fast, Medium and Slow), speed may be further enhanced by selecting for "STOP AT FIRST MATCH (SFM)" as opposed to "ALL AGAINST ALL COMPARISONS". SFM option stops further comparisons as soon as the first match conforming to any of the RISCI alignment signatures is found. To avoid orientation bias, the control shifts between plus and minus hits every 15 hits. The scoring scheme becomes redundant since only one match is allowed, and hence duplications cannot be identified with SFM option.
  2. Medium speed option with SFM off and merger on is recommended.