• 3DCoffee

  • Referenced in 7 articles [sw12008]
  • combining protein sequences and structures within multiple sequence alignments. Most bioinformatics analyses require the assembly ... multiple sequence alignment. It has long been suspected that structural information can help to improve ... order to generate high-quality multiple sequence alignments. 3DCoffee is based on TCoffee version ... pairwise structure comparison methods to generate multiple sequence alignments. We benchmarked 3DCoffee using a subset...
  • HHpred

  • Referenced in 7 articles [sw17271]
  • single query sequence or a multiple alignment as input. Within only a few minutes ... HHpred can produce pairwise query-template alignments, multiple alignments of the query with...
  • I-TASSER

  • Referenced in 18 articles [sw17207]
  • three-dimensional (3D) atomic models from multiple threading alignments and iterative structural assembly simulations...
  • DIALIGN-TX

  • Referenced in 7 articles [sw12751]
  • progressive approaches for segment-based multiple sequence alignment. Background: DIALIGN ... reimplementation of the multiple-alignment program DIALIGN. Due to several algorithmic improvements, it produces significantly ... better alignments on locally and globally related sequence sets than previous versions of DIALIGN. However ... straight-forward greedy approach to assemble multiple alignments from local pairwise sequence similarities. Such greedy...
  • CAP3

  • Referenced in 17 articles [sw08935]
  • overlaps between reads, construction of multiple sequence alignments of reads, and generation of consensus sequences...
  • FUGUE

  • Referenced in 9 articles [sw16894]
  • FUGUE uses the global-local algorithm to align a sequence-structure pair when they greatly ... SSEs. (3) Combined information from both multiple sequences ... multiple structures. FUGUE is designed to align multiple sequences against multiple structures to enrich ... FUGUE improves both homology recognition performance and alignment accuracy...
  • SABmark

  • Referenced in 9 articles [sw17111]
  • Alignment Benchmark (SABmark) provides sets of multiple alignment problems derived from the SCOP classification. These...
  • COMPASS

  • Referenced in 9 articles [sw23109]
  • COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance ... novel method for the comparison of multiple protein alignments with assessment of statistical significance (COMPASS...
  • Probalign

  • Referenced in 7 articles [sw24613]
  • Probalign: multiple sequence alignment using partition function posterior probabilities. MOTIVATION: The maximum expected accuracy optimization ... criterion for multiple sequence alignment uses pairwise posterior probabilities of residues to align sequences ... generally more accurate than other leading multiple sequence alignment methods (i.e. Probcons, MAFFT and MUSCLE...
  • MARNA

  • Referenced in 5 articles [sw35539]
  • MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons. Results ... describe a novel approach for multiple alignment of RNAs (MARNA) taking into consideration both ... system, which is a consistency based multiple alignment method. Furthermore, we are able to extract ... consensus-sequence and -structure from a multiple alignment. We have successfully tested MARNA on several...
  • HMMER

  • Referenced in 19 articles [sw10514]
  • either a single protein sequence, multiple protein sequence alignment or profile HMM against a target ... user expertise and accepts batch uploading of multiple queries at once. All search methods...
  • STAMP

  • Referenced in 6 articles [sw17264]
  • against databases of known motifs; the software aligns input motifs against the chosen database ... discovered motifs. STAMP also automatically builds multiple alignments, familial binding profiles and similarity trees when ... local or global, gapped or ungapped), multiple alignment strategies and tree-building methods. Motifs...
  • IsoRank

  • Referenced in 13 articles [sw08324]
  • describe an algorithm for global alignment of multiple protein-protein inter- action (PPI) networks ... field has focused on local network alignment. The intuition behind our algorithm is that...
  • Rose

  • Referenced in 8 articles [sw16613]
  • history is logged and the `correct’ multiple sequence alignment is created simultaneously. The model also ... evaluation of methods in multiple sequence alignment computation and the prediction of phylogenetic relationships...
  • PROMALS

  • Referenced in 5 articles [sw22476]
  • server for accurate multiple protein sequence alignments. Multiple sequence alignments are essential in homology inference ... server that constructs multiple protein sequence alignments using PROMALS, a progressive method that improves alignment...
  • JPred

  • Referenced in 7 articles [sw35977]
  • server allows a single sequence or multiple alignment to be submitted, and returns predictions from ... prediction algorithms that exploit evolutionary information from multiple sequences. A consensus prediction is also returned...
  • Mugsy

  • Referenced in 4 articles [sw16994]
  • Mugsy: fast multiple alignment of closely related whole genomes. Motivation: The relative ease ... data requires tools that can quickly compare multiple whole-genome sequences, millions of base pairs ... evolution. Results: We present a new multiple alignment tool for whole genomes named Mugsy. Mugsy ... fastest program evaluated for the multiple alignment of assembled human chromosome sequences from four individuals...
  • Soap

  • Referenced in 38 articles [sw08915]
  • program SOAP for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences ... computing, and has a batch module for multiple query sets...
  • PSICOV

  • Referenced in 6 articles [sw17010]
  • sparse inverse covariance estimation on large multiple sequence alignments. Motivation: The accurate prediction of residue ... made by identifying correlated mutations within multiple sequence alignments (MSAs), most commonly through the information...
  • GeneMarkS

  • Referenced in 6 articles [sw23024]
  • coding regions and the Gibbs sampling multiple alignment program. GeneMarkS predicted precisely...