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Taken as a whole, these issues further emphasize the need to continue to improve algorithms for the detection and alignment of these interesting genomic changes.
Our framework is modular in nature and can be readily integrated with other methods for the detection and alignment of TEs in genomic sequences.
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2. Bietz S, Rarey M. ASCONA: Rapid detection and alignment of protein binding site conformations.
The code for the peak detection and alignment algorithms runs in MatLab® Version R2008a.
The acquired raw data files were analyzed by the MarkerLynx application manager version 4.1 for peak detection and alignment, parameters of which were set as formerly reported [ 18].
Inputs for the alignment software were chromatograms of ten different individuals analysed both spiked and non-spiked (see " Control samples" for details) and the set of parameters for peak detection and alignment.
Additionally, it can be used for processing of liquid chromatography/mass spectrometry (LC-MS) data for peak detection, peak picking, and alignment of glycans based on retention time, precursor m/z values, and observed intensities across multiple samples.
miR-100/10 family homologue detection and alignment.
This workflow utilizes the XCMS Centwave algorithm for peak detection and mzMatch.R for alignment of samples, filtering, and metadata storage in peakML files.
Similarities in sequences are scored in a matrix, and the algorithm allows for the detection of gaps in sequence alignment.
Based on the results of the calibration and false positive screen, we formulated a simple protocol for the detection of HEAT and ARM repeats in multiple sequence alignments (Fig. 7, see also Methods).
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