With our data this approach yielded a nearly identical final read set as using the Xenome [ 18] protocol, designed specifically for xenograft sequencing data, with over 98% overlap in each sample.
SOMA [ 9] is another alignment tool designed specifically for aligning sequence contigs from a genome assembly to a consensus optical map.
Results: We developed a new de novo assembler called IVA (Iterative Virus Assembler) designed specifically for read pairs sequenced at highly variable depth from RNA virus samples.
First, it is designed specifically for fungus genome sequences.
In order to combine mathematical modeling with these data and enable experimentally-based modeling, we develop a statistical framework that is designed specifically for time-course RNA sequencing data and, further, we elaborate the statistical techniques that are essential for obtaining our results.
The PHASE software package allows phylogenetic tree construction with a number of evolutionary models designed specifically for use with RNA sequences that have conserved secondary structure.
The commercial FlexMAP tag sequences were not designed specifically for MLPA assays, and some tag sequences, when attached to the default right primer, will form significant secondary structure on their own.
It must be noted that primers utilized for our gene expression studies were designed specifically for detection of human gene sequences.
Several of these have been designed specifically for the visualization of genome sequence assemblies, including EagleView (Huang and Marth, 2008), HawkEye (Schatz et al., 2007) and Tablet (Milne et al., 2010).
Large sets of oligonucleotide probes may be designed specifically for individual exons and/or splice junction sequences, which allow the identification of new AS events.
