Sentence examples for alignment package from inspiring English sources

The multiple alignments were generated by PSI-Coffee, an aligner within the T-Coffee multiple alignment package that aligns distantly related protein sequences using homology extension [ 83, 84 ].

The proteins in each group were aligned using the Darwin multiple sequence alignment package (Gonnet, Hallett, et al. 2000; Gonnet, Korostensky, and Benner 2000).

Putative filozoan KLF/SP and nonfilozoan amorphean KLF-DBD amino acid sequences were aligned using default settings of the MUSCLE alignment package in CLCBio (Edgar 2004).

The reverse complement of each miRNA was then aligned with its validated target regions using the ClustalW alignment package [ 25].

Another approach used to separate contigs from different genomes was to align the contigs to a set of reference sequences using the Exonerate sequence alignment package (v2.2.0; Slater and Birney 2005).

Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.

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'.

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

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

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.