Sentence examples similar to using the following alignment from inspiring English sources

In this work, we predict the TM-score using the following alignment-dependent features: sequence identity, distribution of various per-position scores such as mutation score, solvent accessibility score, secondary-structure similarity score and distribution of gap sizes.

The 2,404 miRNA sequences were aligned using ClustalX [ 43] with the following alignment parameters: gap opening, 22.50; gap extension, 0.83; and bootstrap value, 100.

For in-house genomes, SNP calls were then made by using SolSNP version 1.1 with the following alignment limits: minimum coverage of 20, minimum mapping qualities of 20, and a filter call of 0.95.

The Greengenes 16S rRNA gene database was used for 16S rRNA phylogenetic analysis with the following alignment parameters: >97% identity, minimal alignment 40 bp.

The filtering process is used to efficiently eliminate most of the unrelated reads to speed up the following alignment process.

Scalpel (v0.1.1) was used as a representative of assembly-based callers to assemble the reads and call INDELs from each alignment separately, resulting in 20 INDEL call sets from these 20 alignments, using the following parameter settings: '--single --lowcov 1 --mincov 3 –outratio 0.1 --numprocs 10 –intarget'.

All TcSNP alignment identifiers mentioned in this work (e.g. tcsnp:438249) can be accessed using the following standard URI, and replacing the alignment identifier (e.g. 438249) in each case: http://snps.tcruzi.org/genes/alignment?assembly_id=438249.

Bayesian posterior probabilities were calculated for all alignments using the following parameters on the program MrBayes 3.2.2 (GTR [Lset nst = 6]; gamma distribution [of rate among sites]; and Monte Carlo Markov Chains [starting trees = 4; heating (nchains = 4), default temperature = 0.2; generations = 6,000,000; sample frequency = 100; prior burn-in = 500,000 trees] [ 40, 41].

Local re-alignment around indels was performed on alignments lacking duplicates using the following GATK tools: RealignerTargetCreator, IndelRealigner and FixMateInformation.

Genomic alignments were processed using the following protocol.

These alignments were fed into the RNAz algorithm and rescored using the following parameters.