Sentence examples for sites alignment from inspiring English sources
To visualize the proximity of the significant CpG islands from the transcription and translation start sites, alignment of the EpiTYPER target sequence with the appropriate NCBI nucleotide sequence using ClustalW2 software (http://www.ebi.ac.uk/Tools/clustalw2/index.html) was performed.
Without conserved sites, alignment of the DNA sequences is problematical at best, and could lead to false phylogenetic signal [ 23].
The CRE sites alignment was performed through the MUSCLE [ 108] and the result was visualized using Weblog 3.2 [ 109].
The output page lists putative target genes, miRNA binding sites, alignment scores, and the number/type of mismatches.
3. Open the page with the ABC0302 binding sites alignment (http://regtransbase.lbl.gov/cgi-bin/regtransbase?page=show_alignment& matrix_id=95).
Starting with the highest variability sites, alignment positions were serially removed from the full alignment in 100 site partitions using the script sorter.pl, resulting in two series of data partitions.
Z-score indicates how many standard deviations the current alignment score differs from the average Z-score, calculated from all binding sites alignments over the entire PDB [19].
Afterwards, the resulting structures are being aligned with our new active site alignment algorithm ASCONA [2] which has been developed with a focus on an accurate detection of protein backbone variations.
Furthermore, it also includes structural bioinformatics solutions for inverse screening, binding site alignment, and searching interaction patterns across structure libraries.
In this approach, bioisosteric replacements are identified using local binding site alignment algorithm ProBiS [15 19], which enables identification of locally similar binding sites irrespective of proteins' folds or amino acid sequences.
Based on the active site alignment, a further step detects flexible regions within the binding site and uses a remaining rigid core for a superimposition of the generated ensemble.
