Sentence examples for templates with sequence from inspiring English sources

To make a strict test, we only include template proteins released before May of 2006 for this test, and we also excluded the templates with sequence identity >20% to the query.

We note that the homology exclusion cutoff used here is more stringent than that used by Bradley et al [ 13], who only excluded templates with a PSI-BLAST E-value < 0.05 but without sequence identity cutoff, and that used by Zhang et al [ 12], who only excluded the templates with sequence identity > 30% but without PSI-BLAST checking.

For each sample, gene expression PCR was carried out using 2 µl of cDNA template with sequence specific primers.

If a structure template with sequence identity of >50% is found for a query protein, homology modeling could be chosen as the best in silico method with an accuracy equal to low-resolution X-ray predictions [ 9].

The extracted amount of gDNA was used as a template with sequence-specific primers mentioned below in Table 2 to begin the process of cloning of SPT15 and TAF23 genes in this study.

However, suppose that there were no templates with >90% sequence identity.

Removal of redundancy, i.e. models originating from templates with same sequence, and removal of obvious incorrect oligomeric states upon visual inspection resulted in a set of 557 models, 386 with helical transmembrane parts and 171 β-barrels.

The most successful type of structure prediction, known as homology modeling, relies on the existence of a "template" structure with sequence similarity to the protein being modeled; structural genomics' goal is to provide sufficient representation in solved structures to model most of those that remain.

First, MUSTER, PPI-1, SAM-T02 and PROSPECT2 use an internal I-TASSER template library with sequence identity <70% from http://zhanglab.ccmb.med.umich.edu/library/; SPARKS2 and SP3 use another internal library of sequence identity <40%; HHSEARCH uses the library downloaded from ftp://ftp.tuebingen.mpg.de/pub/protevo/HHsearch/databases, which has also a 70% sequence identity cut-off.

Therefore, to greatly enlarge the pool of useful models, it is essential to improve fold recognition and alignment method for the sequence and template with <30% sequence identity.

PSI-BLAST outputs were filtered using BlastProfiler [40] to select templates with the highest sequence coverage and sequence identity.