Sentence examples for assembled aligned from inspiring English sources

The choice to tailor CodingQuarry to the prediction of fungal genes and to use assembled, aligned transcripts rather than raw read alignments relates to some key differences between fungal genomes and those of higher eukaryotes.

Chromatographs were visualised, inspected, assembled, aligned with related sequences and analysed using the CLC Main Workbench 5.5 (CLC bio, Denmark).

Sequences were checked manually, assembled, aligned, and annotated in Geneious Pro 5.4 [ 39].

Sequence reads derived from both strands were assembled, aligned, and analyzed for nucleotide differences using Sequencher v4.8 (GeneCodes).

CodingQuarry is a highly accurate, self-training GHMM fungal gene predictor designed to work with assembled, aligned RNA-seq transcripts.

The sequencing results were assembled aligned and visualized using the CodonCode Aligner software Version 2.06 (http://www.codoncode.com/).

The resulting alignment data from Tophat were then fed to an assembler Cufflinks (version 2.0.1) to assemble aligned RNA-Seq reads into silkworm genome database (silkworm_glean.gff) and silkworm gene database (silkgenome.fa).fa

The resulting alignment data from TopHat2 were then fed into Cufflinks (v 2.0.2) to assemble aligned RNA-Seq reads into transcripts for each rat individually.

Subsequently, the Cufflinks software [ 80]; version 2.0.2) was used to assemble aligned RNA-seq reads into transcripts with the parameters "--min-intron-length 10"; these assemblies were processed into a full transcriptome set by CuffMerge [ 81].

Cufflinks tools [ 18] version 2.1.1 were then used to assemble aligned RNA-seq reads into transcripts, estimate their abundances, and test for differential expression and regulation [ 18].

BAM files generated using TopHat were uploaded into the Cufflinks transcriptome identification tool [ 28], to assemble aligned RNA-Seq reads into predicted transcripts and calculate relative abundances.