Sentence examples for using a spliced alignment from inspiring English sources

Expressed sequences are compared to the human genome to find high quality hits, and are then aligned to it using a spliced alignment model that allows long gaps, for modeling introns.

An alternative strategy is to map the reads onto the genome using a spliced alignment tool such as TopHat [ 21], as done, e.g., in [ 19, 20].

ACT-Graph edges and weights: (i) a splice edge is inferred from a spliced alignment.

The FL-cDNAs that were not fully integrated into gene structure annotations include aberrantly spliced transcripts, antisense mRNAs, polycistronic mRNAs, mRNAs encoding short, partial or unidentifiable ORFs, mRNAs with non-consensus splice sites, and mRNAs that did not align well to the genome using the spliced alignment utilities employed.

They typically start by mapping sequencing reads onto the reference genome, using spliced alignment tools, such as TopHat [ 29] or SpliceMap [ 30].

The transcripts were aligned on the genome using PASA [ 42], an eukaryotic genome annotation tool that uses spliced alignments of transcript sequences to automatically model and update gene structures.

In a series of tests, Splign has produced more accurate results than other tools commonly used to compute spliced alignments, in a reasonable amount of time.

GeneWise67 (with parameter -trev -sum -genesf) was used to predict spliced alignments.

Seed and extend strategy is one of the most popular heuristic algorithms; here we use it to solve spliced alignment problem.

We also explored an alternative, spliced alignment strategy for finding TICs by identifying splicing events within individual reads using our GSNAP program [ 27].

At the third level, the analytical steps specific to each application are used for classification (quality control, spliced alignment, de novo assembly, etc.; Figure 1B).