Structures predictions were performed by the MODELLER software 24, 25 using the optimal multiple template of the HHpred server.
(iii) We can use multiple templates for dealing with change of target appearance.
For taxa where direct sequencing was impossible due to the presence of multiple templates, cloning of the 1,000 bp fragment was carried out prior to sequencing using the TOPO TA® method (Invitrogen).
Making a method available that can readily use multiple templates is of great importance, particularly since there is not an abundance of such methods available as web servers.
In the annotation system where the multiple templates comprised of the species i ∈{ Arabidopsis, rice, maize, castor bean, potato} were employed to identify the function of a query sequence, the definitions of MS and CS are given as follows: (1) MS = ∑ i N m H i × F i N m, (2) CS = ∑ i N m H i × F i N t.
In addition, the bank of multiple templates allow the statistics of the expected event waveform characteristics and time courses to be derived, and detection thresholds and safeguards against false detection to be subsequently set in a statistically meaningful manner.
When a read was mapped to multiple templates, a coefficient of 1/(the number of different templates) was given for each template.
BCCP domain of ACCA3 (Rv3285) protein of Mtb was modeled by MODELLER 9v6 [36] based on its homology with multiple templates (Figure 9) of known NMR or crystal structures of BCCP or BCCP containing proteins (E. coli BCCP 1bdo, Propionibacterium shermanii transcarboxylase:1dcz, Bacillus subtilis BCCP 1z7t, P. horikoshii BCCP 2d5d and Human acetyl Co-A carboxylase:2ejm).
Consequently, we suggest that the use of multiple templates when building comparative models of GPCRs is likely to lead to more accurate results.
