Sentence examples for multiple alignment models from inspiring English sources

Another reason for putative phosphorylation sites being mapped to incompatible residue types is that automatic transfer of the modification annotation onto other sequence records depends on the accuracy of the multiple alignment models that define the domains.

To describe our original multiple alignment model, we begin by noting that, given a topology τ, the multiple alignment A can be decomposed into a set of pairwise alignments A(b ) along each branch b of the topology.

All gene models were manually refined based on the AA-BB-BBCC-CC multiple alignment framework.

The Conserved Domain Database (CDD), part of NCBI's Entrez database system, is a protein annotation resource that consists of a collection of well-annotated multiple sequence alignment models as position-specific score matrices (PSSMs) [ 19].

Sites are recorded as addresses on the multiple sequence alignment models that describe the domain family, and this mapping is being transferred into the coordinates of the PSSMs that are used to scan the protein sequence database.

URL: http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi The Conserved Domain Database (CDD) (1) consists of a collection of well-annotated multiple sequence alignment models for ancient domains and full-length proteins.

Results were inputted into MODELLER [ 34] using a multiple alignment for modeling of the tertiary structure.

Therefore, an effective parallel multiple sequence alignment model capable of resolving these issues is in a great demand.

The templates were superposed using the MALIGN3D command of MODELLER [36] to generate structure-based multiple alignments for modeling the remaining 11 yBRDs.

We used the information in the reference multiple alignment to build a model of the protein family and sequences that deviated from this model were annotated as having potential sequence errors.

From this multiple alignment a hidden Markov model (HMM) was constructed [ 50].