Sentence examples for search seed from inspiring English sources

PhymmBL version 3.2 uses a more sensitive search seed size of 11, which is more computationally costly.

Using this REase aa sequence as a search seed revealed a closely-related RM system lacking a C gene in the Gram-positive genus Streptococcus.

The BLAST results shown in Figure 6 use a search seed size of 28 (the current default setting) and are thus tuned for speed.

We used the amino acid sequence of R.PvuII (gi 135242) as the search seed (initial query), and examined all available bacterial and archaeal genome sequences (complete and shotgun) using the program TBlastN [ 36].

PhymmBL jobs did not complete within 48 h on the smallest timing dataset (using 80 threads) underscoring our expectation that BLAST-based approaches with the smaller search seed size do not scale for this problem.

To confirm this result, we used a five iteration PSI-BLAST search using both the B. cereus folB gene and the folB domain of the D. purpureum folB-folK-folP gene fusion as a search seed against the NCBI GenBank nonredundant (NR) protein database (performed both as a general search and a search restricted to eukaryotic taxa).

Furthermore, using these fused genes as search seeds, we identified three additional RM systems.

Results of the HHpred search seeded with TP1 (A) and gp7 (B) sequences.

Results of the HHpred search seeded with the putative capsid protein of Southern tomato virus (YP_002321510).

Chloroplast contigs were extracted using a BLAST search seeded with the Morus indica L. (Moraceae) chloroplast genome (GI: 89,574,460).

In the seed search, seeds of query subsequences and representative subsequences in the database are found using B e and B r.