Figure 1.
The flow of GHOSTX.
Figure 2.
Seed search algorithm using suffix arrays.
Figure 3.
Search algorithm using a suffix array.
Figure 4.
An example seed search.
Figure 5.
Conditions for reducing seeds in chain filtering.
Figure 6.
Search sensitivity of each tool with KEGG GENES.
The vertical axis shows the percentage of correct answers that correspond to the correct answers for each method. The horizontal axis shows the E-value of the alignments.
Table 1.
Computation time with SRS011098 and KEGG GENES (3.9 GB).
Table 2.
Computation time with SRR444039 and KEGG GENES (3.9 GB).
Table 3.
Computation time with SRS011098 and NCBI nr (14.8 GB).
Table 4.
Computation time with SRR444039 and NCBI nr (14.8 GB).
Table 5.
Computation time of the preprocessing including indexing with KEGG GENES (3.9 GB) and NCBI nr (14.8 GB).
Figure 7.
Computation times with multithreading.
Table 6.
Comparison with memory size for KEGG GENES (3.9 GB) of each size of the database chunks.
Table 7.
Comparison with Computation time for KEGG GENES (3.9 GB) of each size of the database chunks.