However, in some cases we obtained significant homology against the D. pulex genome database for contigs that had no homology in any of our other method-database combinations.
However, in comparison of results from the 2007 and 2008 updates of the UniProt database, we observed a greater percentage of matches in the 2007 search (Table 6), but a much greater number of homology matches during the 2008 search that had no homology in other method-database combinations.
Overall, of the clones with strong homology, 74% can be considered robust matches, as from four to six homology search method-database combinations returned matches, thus about 49% of our library has robust annotation, about 17% has annotation that likely will require further analysis, and 34% has no annotation.
We searched the genomes for homologs using the Smith-WatermanP algorithm [ 22] on a TimeLogic DeCypher in all query-database combinations (matrix: Blosum62; e-value cutoff:100).
The specific program-query-database combinations used for each search are shown in Table 3. BLAST programs were run using a series of E-value thresholds, from E-value ≤ 1 to E-value ≤ 0.00001, with default parameters and without low-complexity filtering.
The search terms were adapted for use with other bibliographic databases in combination with database-specific filters, where these were available.
We provide the first global evaluation of the trends, drivers, and population and ecosystem consequences of invertebrate fisheries based on a global catch database in combination with taxa-specific reviews.
" database:entry ": combination form of database name and index ID.
They also illustrate the types of useful information that can be extracted from the database in combination with the DNPTrapper software.
Syntenic genes to Wnt5 paralogs were identified using the same version of Ensembl database in combination with the ortholog identification method [ 44- 46].
