Sentence examples for smart database and from inspiring English sources

To this end, we extracted a number of SET domain genes from human (47), Drosophila (29), C. elegans (30), S. pombe (11) and S. cerevisiae (7) through analyses of SMART database and NCBI protein database (Table S1).

Domain information of each protein was collected from the SMART database and a HTML based visualization tool was developed, to display this knowledge.

Each calpain-like sequence was then searched against the protein conserved domain database (CDD), SMART database and the Pfam database to annotate domain modules [ 47- 49].

DOI: http://dx.doi.org/10.7554/eLife.04726.006 Calponin homology domains are widespread in the human genome (157 domains referenced in SMART database) and are classified in three classes CH1, CH2 and CH3.

We found a previously unreported DEP- like fragment (DLF) domain, recognized by the SMART database, and is present and conserved in several nematode species from clades 8, 9, and at least one species, S. carpocapsae, from nematode clade 10.

Sequences of the catalytic domains (about 280 aa in length) and additional domains used for phylogenetic tree construction were obtained from the SMART database and sequences with poor instances of Motif I and XI were checked manually.

To verify the reliability of our results, each sequence was then searched against the protein conserved domain database (CDD) [ 16], SMART database [ 17], and the PFAM database [ 18], respectively.

While the SMART searches use the underlying SMART database, which consists of manually annotated protein profiles [ 110], the NCBI-CDD search hosts multiple databases, including CDD profiles v3.13.

The Pfam http://www.sanger.ac.uk/Software/Pfam/ and SMART database http://smart.embl-heidelberg.de/smart/batch.pl were finally used to confirm each predicted WD40 protein.

Predicted transmembrane structures were obtained using the transmembrane prediction server TMHMM-2.0 http://www.cbs.dtu.dk/services/ and SMART database http://smart.embl-heidelberg.de/ with the complete protein sequences.

Then, the online software Conserved Domain Database of NCBI (http://blast.ncbi.nlm.nih.gov) and SMART database (http://smart.embl-heidelberg.de/) were used to further confirm the predicted MAPK cascade genes.