• PatternHunter

  • Referenced in 36 articles [sw20963]
  • PatternHunter: faster and more sensitive homology search. MOTIVATION: Genomics and proteomics studies routinely depend ... homology searches based on the strategy of finding short seed matches which are then extended ... growth presents a dilemma for DNA homology search techniques: increasing seed size decreases sensitivity whereas ... computation. RESULTS: We present a new homology search algorithm ’PatternHunter’ that uses a novel seed...
  • Infernal

  • Referenced in 12 articles [sw17000]
  • Infernal 1.1: 100-fold faster RNA homology searches. Summary: Infernal builds probabilistic profiles ... given as input. Infernal uses CMs to search for new family members in sequence databases ... filter pipeline for RNA homology search based on accelerated profile hidden Markov model (HMM) methods...
  • QPath

  • Referenced in 11 articles [sw35403]
  • interest, our algorithm, QPath, efficiently searches the network for homologous pathways, allowing both insertions ... protein pathways in fly. Conclusion: Pathway homology searches using QPath provide a powerful approach...
  • FASTA

  • Referenced in 25 articles [sw09655]
  • sequences that are homologous to the query sequence, or the search will result...
  • RSEARCH

  • Referenced in 10 articles [sw23815]
  • RSEARCH: finding homologs of single structured RNA sequences. BACKGROUND: For many RNA molecules, secondary structure ... been published that allow searching a sequence database for homologs of a single RNA molecule ... local alignment algorithm to search a database for homologous RNAs. For this purpose, we have ... which RSEARCH outperforms the primary sequence search programs BLAST and SSEARCH. The primary drawback...
  • CMfinder

  • Referenced in 6 articles [sw17265]
  • novel integration of multiple techniques for effective search of motif space, and a Bayesian framework ... model can be directly used for homology search, allowing iterative refinement of structural models based...
  • FragGeneScan

  • Referenced in 4 articles [sw17159]
  • genes identified by homology search), and many novel genes with no homologs in current protein...
  • LocARNAscan

  • Referenced in 2 articles [sw23118]
  • sequence and structure-based RNA homology search. BACKGROUND: The search for distant homologs has become ... families unrelated by common descent. Current homology search tools for structured RNAs are either based ... secondary structure alone informative for homology search and the detection of novel members ... demonstrate that a purely structure-based homology search is feasible in principle, it is unlikely...
  • FastLSA

  • Referenced in 3 articles [sw01958]
  • alignment is a fundamental operation for homology search in bioinformatics. For two DNA or protein...
  • PRALINE

  • Referenced in 2 articles [sw16248]
  • PRALINE can integrate information from database homology searches to generate a homology-extended multiple alignment...
  • DbClustal

  • Referenced in 2 articles [sw33970]
  • alignments of protein sequences detected by database searches. DbClustal addresses the important problem ... length sequences detected by a database homology search. By combining the advantages of both local...
  • piRNABank

  • Referenced in 2 articles [sw23005]
  • features: Simple search; Search piRNA clusters; Search homologous piRNAs; piRNA visualization...
  • ESyPred3D

  • Referenced in 5 articles [sw16876]
  • ESyPred3D: Prediction of proteins 3D structures. Motivation: Homology or comparative modeling is currently the most ... four steps: (1) databanks searching to identify the structural homolog, (2) target–template alignment...
  • piRNAQuest

  • Referenced in 1 article [sw23007]
  • piRNAome for silencers. An integrated resource for searching the piRNAome of human, mouse ... cluster. Several analysis tools like Homology search within annotated piRNAs, Dynamic piRNA Clusters, Pattern Search...
  • VaZyMolO

  • Referenced in 1 article [sw16899]
  • unit. Modules were first identified by homology search and then validated by the convergence...
  • PROMALS

  • Referenced in 5 articles [sw22476]
  • alignment quality by using additional homologs from PSI-BLAST searches and secondary structure predictions from...
  • ProTherm

  • Referenced in 9 articles [sw16247]
  • links to homologous structures to each protein. Further, we have improved the search and display...
  • PROMALS3D

  • Referenced in 3 articles [sw16918]
  • structural information from database searches. PROMALS3D automatically identifies homologs from sequence and structure databases...
  • HadamardSearch

  • Referenced in 10 articles [sw18675]
  • finite group G for which a homological model hG is known, as described by V.Alvarez ... Hadamard matrices in Mathematica: exhaustive and heuristic searches”, ICMS-06, Castro Urdiales, Spain...
  • CUDAMPF++

  • Referenced in 1 article [sw21326]
  • Proactive Resource Exhaustion Scheme for Accelerating Homologous Sequence Search on CUDA-enabled GPU. Genomic sequence ... widely used for the analysis of homologous protein and nucleotide sequences with high sensitivity, based...