Sentence examples for by submitting the alignment from inspiring English sources

A phylogenetic tree was constructed by submitting the alignment in Fig. 3 to the "Mr. Bayes" software ([32], using a "mixed protein" model).

DBL5ε homology models were created by submitting the multiple alignment to the HHpred server [38].

Adequate parameters for phylogeny inference were obtained by submitting the produced alignment to the ProtTest evolutionary model selection software [23].

The sequence logos for R2 and R3 MYB repeats were created by submitting the multiple alignment sequences to the WebLogo server (http://weblogo.berkeley.edu/logo.cgi) [ 73].

Multiple sequence alignment was performed by submitting the non-coding sequences to MLAGAN (Multi-LAGAN, Multi-Limited Area Global Alignment of Nucleotides) (Brudno et al, 2003), which is compatible with the VISTA visualisation tool.

The search space consists of clusters of reads directly characterized using the taxa of proteins of those high-quality alignments, which are obtained by submitting the reads as BLASTx queries.

The multiple sequence alignments for each family were created by submitting the sequences to the MAFFT ver.6 server (http://mafft.cbrc.jp/alignment/server/index.html) using the E-INS-i strategy.

The resulting alignment was aligned to the six PUR repeats by submitting both multiple alignments to HHalign on the Bioinformatics toolkit.

rVISTA 2.0 searches for conserved TFBSs were performed against 500 vertebrate TF matrices from the TRANSFAC library, with matrix similarity cuttoff 0.85 by submitting a BLASTZ alignment file for each CNE to the rVISTA 2.0 site.

Diverse conformations within 20 kcal/mol energy range were generated and submitted to the alignment procedure.

Conformations within 20 kcal/mol were submitted to the alignment procedure.