Sentence examples for using a gapped alignment from inspiring English sources

Longer reference sequences such as repeats and hairpin precursors were mapped to the tammar genome using a gapped alignment tool similar to BLAST.

Once the results were filtered, we created a gapped alignment using the Gap22 program [ 48] on segments for which the identity was greater than 85%.

Reads were then realigned to the subsection of the genome using a gap-aware alignment program, cross_match (http://www.phrap.org/phredphrapconsed.html).html

The final alignment is being done using the Gotoh [ 38] algorithm, a dynamic programming algorithm used for gapped alignment.

We start by mapping each read to the reference genome in standard fashion using gapped alignment.

New transcript sequences were then extracted and further assembled by Sequencher software (Gene Code Inc. USA) using gapped alignment.

To evaluate the expression of unigenes, we first mapped trimmed reads to unigene sequence using gapped alignment mode of the program Bowtie 2.2.1.0 (Langmead et al. 2009).

Previous report by Ner-Gaon et al. suggested a 3.7-fold difference in AS rates between O. sativa and S. bicolor using EST pairs gapped alignment [ 26].

The blastp algorithm used gapped alignment with the following parameter: expectation value 10-300), open gap (−1), extend gap (−1), threshold for extending hits (11) and word size (3).

It then determines the possible location of gaps in the alignment based on splice junctions flanking the aligned reads and uses gapped alignments to align the reads that were not aligned by Bowtie in the first step.

A recent study using EST pairs gapped alignments (EST-EST) surveyed 11 plant species and suggested that overall AS frequencies vary greatly in different plant species, with some rates comparable to those observed in animals [ 3].