• Current approaches focus on using heuristics to map reads quickly to large genomes, rather than generating highly accurate alignments in coding regions. (sanbi.ac.za)
  • RAMICS substantially outperforms all other mapping approaches tested in terms of alignment quality while maintaining highly competitive speed performance. (sanbi.ac.za)
  • We show how the use of Intel tools such as Pintools, VTune™ tools, and the Intel® Cilk™ language allow analyzing and optimizing the performance of the widely-used BWA aln program for alignment. (intel.com)
  • One of the initial goals of the ExaScience Life Lab is to examine how supercomputers can accelerate the processing of whole-genome sequences. (intel.com)
  • This article focuses on recent advances of the ExaScience Life Lab in optimizing the alignment phase of whole-genome processing. (intel.com)
  • With the high number of genome sequences currently in the public databases, the risk of transitive annotation errors is high. (geneontology.org)
  • Using this paper as a reference, it was straight forward to add the required OpenMP code to the most recent version of Clustal (I only modified the first stage pairwise alignment portion of the code). (bioinformatics.org)
  • Residues that are conserved across all sequences are highlighted in grey. (wikipedia.org)
  • In almost all sequence alignment representations, sequences are written in rows arranged so that aligned residues appear in successive columns. (wikipedia.org)
  • Mathematica 7 adds industrial-strength state-of-the-art sequence analysis tools. (wolfram.com)
  • SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. (nih.gov)
  • a ) Alignments of one pair of reads and three single-end reads. (nih.gov)
  • This approach facilitates the generation of highly accurate alignments, accounting for the error biases of the sequencing machine used to generate reads, particularly at homopolymer regions. (sanbi.ac.za)
  • However, most interesting problems require the alignment of lengthy, highly variable or extremely numerous sequences that cannot be aligned solely by human effort. (wikipedia.org)
  • The process of evaluating a sequence alignment involves checking that the length of the matching region and the percent identity with the matching sequence are sufficient to infer shared function. (geneontology.org)
  • The experimentation carried out compare the performance of our method and previous alignment methods. (springer.com)
  • This evaluation may be carried out by the curator, when sequence analysis is performed by the curators, or by authors of a published paper, when the curator is making annotations based on literature. (geneontology.org)
  • Sequence alignments are also used for non-biological sequences, such as calculating the edit distance cost between strings in a natural language or in financial data. (wikipedia.org)
  • T his page presents several data matrices and DNA sequence alignments published or presented by staff and collaborators of the Lewis B. and Dorothy Cullman Program for Molecular Systematics Studies at The New York Botanical Garden. (nybg.org)
  • The input data forpairwise sequence alignment are two sequences S1 and S2. (coursera.org)