PMC:1679804 / 141153-142559 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/1679804","sourcedb":"PMC","sourceid":"1679804","source_url":"https://www.ncbi.nlm.nih.gov/pmc/1679804","text":"Figure 12(a) and 12(b) compare time and memory usage, respectively, for SMOTIF-1, SMOTIF-2 and SMARTFINDER, when searching for the Copia retrotransposon in chromosome 1 of A. thaliana. We can see that SMOTIF-2 is around 5 times faster and takes around 8 times less memory than SMARTFINDER. Their running time and memory usage increase slowly with the number of missing components. This is because in both approaches, the simple motif search step is the same for different number of missing components and usually takes most of the time and memory. SMOTIF-1 always outperforms SMARTFINDER, both in time and memory usage. SMOTIF-1 is more than 7 times faster and takes 100 times less memory than SMARTFINDER! Its time increases linearly with the number of missing components. While SMOTIF-1 is faster when there are no missing components, SMOTIF-2 does better when there are two missing components. This is because SMOTIF-1 does the positional joins on the pos-lists of individual symbols, rather than simple motifs, so over all the sub-motifs of the structured motif, the pos-lists of simple motifs may be redundantly computed several times in SMOTIF-1, whereas these are computed only once in SMOTIF-2. Thus the time of SMOTIF-1 varies depending on the number of missing components. However, since we keep one pos-list per DNA/IUPAC symbol, the memory usage remains almost unchanged for SMOTIF-1 algorithm.","tracks":[]}