Sentence examples for alignment software package from inspiring English sources

To define the discontiguous sequence similarity of two regions R and R', S R, R'), we first applied a popular local alignment software package called CHAOS [ 46] for aligning R and R'.

DNA sequence reads were aligned to the M. xanthus genome [ 10] using the short-read alignment software package Bowtie [ 128].

The software packages and program tools used in this study are: (a) Protein Sequence Alignment software package: BLASTP [ 30, 33].

Furthermore, all analyses critical for our conclusions were repeated using the alignments from a second alignment software package, namely T-Coffee.

Sequence alignment against the 12X V1 coverage, was performed using ELAND, an un-gapped alignment software package, which is part of the Illumina pipeline version 1.32.

We mapped all the public ESTs (2.5 millions ESTs) from dbEST as well as the ESTs from Incyte Genomics' LifeSeq database (5.1 millions ESTs) using a local alignment software package AAT.

In regard to problem (2), we chose the advanced structure matching program SSM, which is considered one of the best current structural alignment software packages [33], [34], [35].

An overview on alignment software packages freely or commercially available can be found in a recent review by Katajamaa et al. [ 6].

Different sequence alignment software packages have attempted to circumvent the challenge of assigning reads that map to multiple sites (termed multi-reads) [ 24- 29].

Since different multiple alignment software packages can yield very different alignments, use of the profile HMM approach is more robust than relying on a single multiple alignment to construct a consensus or a position-specific score matrix.

The Bayesian phylogenetic analysis (Fig. 1C) was performed on the basis of coding nucleotide sequence alignment, using MrBayes software embedded within Geneious package [19], [20].