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Exact(9)
To eliminate the situation that the robot stops before reaching the target position (as shown in Fig. 4), the searching program assumes that the robot cannot move any further and terminates the simulation if the number of switching operations exceeds 10.
We also tried the HHsenser server, another sensitive sequence searching program, which retrieved similar results.
The task of the searching program in each case is to find, preferably, only protein sequences from the test sets in the whole SCOP database, while only providing the corresponding training sets to the searching program.
For each r value, we ran the searching program and calculated the score of the resulting network.
The masses of the tryptic peptides were entered into the MS-Fit database searching program, the results of which can be seen in Table 3 > -wrap-foot>.
a) Score is –10log(p), where p is the probability that the observed match is a random event, based on the NCBI database using the MASCOT searching program as MS/MS data.
Similar(50)
This is usually carried out using sequence similarity searching programs such as BLAST [ 41].
Three motif searching programs have been used for the purpose: MEME [ 22], Weeder [ 23, 24] and AlignACE [ 25].
Comprehensive tests demonstrated that these embedded consensus residues improved performance in readily available sequence query searching programs.
The differences among these three searching programs are mainly due to the parameters used in the respective perl scripts.
It details a search program called X-Keyscore.
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