• STAR

  • Referenced in 14 articles [sw02515]
  • undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix ... arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor...
  • RAPSearch2

  • Referenced in 3 articles [sw23045]
  • substantial memory footprint to identify alignment seeds, due to its use of a suffix array...
  • PMFastR

  • Referenced in 1 article [sw24608]
  • memory consumption allowing for the alignment of large sequences such as 16S and 23S rRNA ... programs. Furthermore, we regenerate 607 Rfam seed alignments and show that our automated process creates ... alignments to the manually-curated Rfam seed alignments...
  • deBGA

  • Referenced in 2 articles [sw30181]
  • deBGA: read alignment with de Bruijn graph-based seed and extension. Motivation: As high-throughput ... data continues to rise, HTS read alignment is becoming increasingly rate-limiting, which keeps pressing ... innovative graph-based seed-and-extension algorithm to align HTS reads to a reference genome...
  • YASS

  • Referenced in 5 articles [sw22992]
  • alignment tool based on an efficient and sensitive filtering algorithm. It applies transition-constrained seeds ... identify groups of seeds that are likely to exhibit significant alignments. A web interface...
  • Repseek

  • Referenced in 3 articles [sw13190]
  • composition biases both at the seed detection and alignment levels...
  • libgapmis

  • Referenced in 2 articles [sw24065]
  • small number of mismatches in the alignment; however, their ability to allow for gaps varies ... seed-and-extend strategy is applied in most short-read alignment programmes. After aligning ... read--the seed--an important problem is to find the best possible alignment between...
  • PASS

  • Referenced in 3 articles [sw35276]
  • programs. PASS performs fast gapped and ungapped alignments of short DNA sequences onto a reference ... index of the genomic positions of ‘seed’ words (typically 11 and 12 bases) as well ... short words (typically seven and eight bases) aligned against each other. After building the genomic ... matching seed words in the genome; (2) for every match checks the precomputed alignment...
  • VSEARCH

  • Referenced in 1 article [sw34388]
  • high speed. VSEARCH uses an optimal global aligner (full dynamic programming Needleman-Wunsch), in contrast ... default uses a heuristic seed and extend aligner. This usually results in more accurate alignments...
  • OMBlast

  • Referenced in 1 article [sw34215]
  • OMBlast: alignment tool for optical mapping using a seed-and-extend approach. Motivation: Optical mapping ... robust and accurate tool called OMBlast for aligning optical maps, the set of signal locations ... based on the seed-and-extend approach from sequence alignment, with modifications specific to optical...
  • MicroStructPy

  • Referenced in 2 articles [sw38257]
  • three critical improvements: (i) allowing for controlled seed overlap to better represent microstructural statistics ... axis aligned bounding box tree structure for accelerated seed placement. Our method recreates a diverse...
  • GASSST

  • Referenced in 1 article [sw34350]
  • filtering step that discards most alignments coming from the seed phase before they are checked ... efficiency to quickly eliminate most candidate alignments in a wide range of configurations. The main...
  • Pash

  • Referenced in 1 article [sw34370]
  • gapped k-mer alignment, a non-seed based comparison method, which is implemented using multi...
  • 3D-hit

  • Referenced in 1 article [sw10913]
  • metric. The best aligned pairs of segments are selected as seeds for futher analysis. Those ... order to construct the global structural alignment by concatenating pairs of matching segments. The method...
  • SpEED

  • Referenced in 2 articles [sw23451]
  • sensitive spaced seeds. Summary: Multiple spaced seeds represent the current state ... applications in various areas such as sequence alignment, read mapping, oligonucleotide design, etc. We present ... program that computes highly sensitive multiple spaced seeds. SpEED can be several orders of magnitude...
  • PROFcon

  • Referenced in 5 articles [sw35542]
  • contact prediction method that combines information from alignments, from predictions of secondary structure and solvent ... Furthermore, predictions are already accurate enough to seed predictions of global features of protein structure...
  • SortMeRNA

  • Referenced in 1 article [sw17152]
  • core algorithm is based on approximate seeds and allows for fast and sensitive analyses ... Optionally, it can provide high quality local alignments of rRNA reads against the rRNA database...
  • Matlab

  • Referenced in 13544 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • R

  • Referenced in 9969 articles [sw00771]
  • R is a language and environment for statistical...
  • CUDA

  • Referenced in 1325 articles [sw03258]
  • The NVIDIA® CUDA® Toolkit provides a comprehensive development...