The SMART oligo sequence (SMART-16attB1-T3: 5'-TACAAAAAAGCAGGCTAATTAACCCTCACTAAAGGG-3') and the overhang of the oligo dT) primer (5'-GGGGACCACTTTGTACAAGAAAGCTGGGCGGCCGC [dT]20VN-3') used for first strand synthesis include an attB1 and attB2 recombination site respectively.
After removing redundant sequences and incomplete ORF sequences, SMART tools (http://smart.embl-heidelberg.de/) and InterProScan (http://www.ebi.ac.uk/Tools/pfa/iprscan/) were used to confirm the presence of the characterized AP2/ERF domain in the candidate sequences.
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Apart from using UniProt sequences and SMART (Simple modular architecture research tool) platform for domain profiling, a set of customized scripts were developed to extract the patterns of protein domain distribution.
At this point, the sequences of SMART [49] family SM00134 were incorporated into the dataset.
A total of 1,878 domains were found for 7,674 protein sequences from SMART database.
To overcome this difficulty, we incorporated tryptic peptides preceding the cleavage sites based on predicted signal sequences from SMART [ 27], SignalP4.0 [ 28], and cleavage sites annotated in HPRD [ 29] into our analysis pipeline.
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These methods allow to remove almost all artifacts on the ECG signal to achieve a better diagnosis and smart sequence synchronization.
SMART sequence analysis (http://smart.embl-heidelberg.de) predicted a transmembrane domain in residues 15 37.
To obtain a longer sequence, Clontech's SMART RACE protocol was used for 3' RACE.
