Sentence examples for alignment packages from inspiring English sources

Additionally, multiple sequence alignment was also performed by sequence alignment packages inbuilt in MEGA 5.10 [ 48].

From their main principles, the three data alignment packages are based upon a similar alignment principle.

Firstly we applied "sequenced based" alignment methods using AQUA [ 39], this incorporated MUSCLE [ 78] and MAFFT [ 79] alignment packages, and a refinement algorithm RASCAL [ 80].

These methods have nonetheless been used to validate all the currently available multiple sequence alignment packages and can certainly be credited (or blamed …) for having re-focused the entire methodological development toward the production of structurally correct alignments.

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 ].

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 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).