Sentence examples for predictions are run from inspiring English sources

The transmembrane region predictions are run through three different programs located at: HMMTOP (http://www.enzim.hu/hmmtop/), SOSUI (http://sosui.proteome.bio.tuat.ac.jp/sosui_submit.html) and TMPRED (http://www.ch.embnet.org/software/TMPRED_form.html).html

Target predictions were run for all predicted miRNAs.

Due to technical problems with the PINUP server, some of the PINUP predictions were run locally using source code and binaries kindly provided by the authors.

All predictions were run on unaligned, ungapped sequences.

Prior to the process of manual annotation an automated analysis for similarity searches and ab initio predictions is run in an extended Ensembl analysis pipeline system [ 49].

When the predictions were run using additional weighting of the amino acids appearing in positions 1 and 4 of the heptad repeat, which helps to rule out false positives, we were unable to confirm the putative coiled coils).

The predictions were run three times using different input evidence datasets: 1) the 9,613 high-confidence Trinity assembled transcripts (see above), 2) all Trinity assembled transcripts, and 3) no assembled transcripts.

Disorder prediction was run on the best model in Phyre2.

Small RNA targets prediction was run against the transcriptome of interest.

iii) A third prediction was run using GeneWise [ 64] to search for all the proteins encoded in several fungal genomes (P. chrysogenum, P. marneffei, T. stipitatus, A. nidulans, Fusarium oxysporum, A. flavus, N. crassa, G. zeae, H. capsulatum) and the set of revised proteins found in Uniprot (as of June 2011).

Since a considerably increase of overlap is obtained among target predictions or validated pairs lists when prediction methods are run using a common source of annotation (24), we designed miRGate database to use a complete dataset built on up-to-date sources that provide full miRNA and 3′-UTR sequences.