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The repeat-masked BESs sequences were searched in model grass genomes by BLASTN against Brcahypodium chromosome 2, rice chromosome 1 and Sorghum chromosome 3 at an e-value of 1e-5 and a minimum hit length of 50 bp.
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These, and the information in the databases they contain, will aid searching in, comparing, and modeling nervous systems at spatial scales from the level of molecules to behavior, in normal, diseased, or injured humans and animals.
The diatom homologs were first searched in filtered models and search was further extended to all models only if the respective homolog was not detected in filtered models.
Hence, it is important to provide means to help designers to search in big models for particular instances of some variable schema of UML models (design patterns) they construct.
Furthermore, sequences are searched in the reduced (five) alphabets model [34] of amino acids.
Our functional annotation was assessed by two strategies: 1) by comparing the domain organization of each protein to annotated proteins sharing the same domain organization in the Pfam database and 2) by searching orthologs in model organisms.
We have achieved this by exploiting parallelism in searching the QSAR model space for the best models.
Next, performing the best warp search in the model space rather than in the feature space [14] further reduces the necessary computational resources for real-time applicability and performance.
Each record and search in the model gets a default view.
A search in the model space was done with a stepwise algorithm.
However, although searches in multiple model species (see details in Material and methods) indeed unearthed some additional sequences, no new subfamilies were detected.
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