Multiple, non-overlapping, local similarity (same algorithm as SIM) Protein sequence to structure alignment that includes secondary structure, structural conservation, structure-derived sequence profiles, and consensus alignment scores Java open-source implementation of Smith-Waterman GPU-based dynamic programming with backtrackingĭoes pairwise sequence alignment with one gap scf) against a template sequence, locate errors, and correct them instantly. Posterior based local extension with descriptive evolution modelĪlign chromatogram files (.ab1. Automatic repetitive sequence filter.īioconductor Biostrings::pairwiseAlignmentĭNA sequence alignment of unrestricted size in single or multiple GPUs Similar alignments are grouped together for analysis. Forrestįor DNA, RNA and protein molecules up to 32MB, aligns all sequences of size K or greater. * Sequence type: protein or nucleotide Pairwise alignment Nameįast heuristic anchor based pairwise alignmentĪlignments for membrane protein sequences Rucci E, García C, Botella G, De Giusti A, Naiouf M and Prieto-Matías M Įnhanced Smith-Waterman on Intel's Multicore and Manycore architectures based on AVX-512 vector extensions Smith-Waterman implementation for Intel Multicore and Manycore architectures Smith-Waterman search, slower but more sensitive than FASTAįirst parallelized algorithm employing the emerging Intel Xeon Phis to accelerate Smith-Waterman protein database searchįirst parallel Smith-Waterman algorithm exploiting Intel Xeon Phi clusters to accelerate the alignment of long DNA sequences Linking and profiling sequence alignment data from NCBI-BLAST results with major sequence analysis servers/services Retrieve and Relate (R&R) is a high performance yet sensitive multi-database search engine, capable of searching in parallel through DNA,RNA and Protein sequences. Li W, McWilliam H, Goujon M, Cowley A, Lopez R, Pearson WR Position-specific iterative BLAST, local search with position-specific scoring matrices, much more sensitive than BLASTĪltschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ Ĭombining the Smith-Waterman search algorithm with the PSI-BLAST profile construction strategy to find distantly related protein sequences, and preventing homologous over-extension errors. Rucci E, García C, Botella G, De Giusti A, Naiouf M, Prieto-Matías M įast Smith-Waterman search using SIMD parallelization OpenCL Smith-Waterman on Altera's FPGA for Large Protein Databases "Search and clustering orders of magnitude faster than BLAST". Steinegger M, Mirdita M, Galiez C, Söding J Įdgar, R.
Similar sensitivity to BLAST and PSI-BLAST but orders of magnitude faster
#CODONCODE ALIGNER TORRENT SOFTWARE#
Software suite to search and cluster huge sequence sets. Hannes Hauswedell, Jochen Singer, Knut Reinert High performance local aligner compatible to BLAST, but much faster supports SAM/BAM High-performance general purpose sequence similarity search tool Pairwise comparison of profile Hidden Markov models very sensitive Local and global search with profile Hidden Markov models, more sensitive than PSI-BLASTĭurbin R, Eddy SR, Krogh A, Mitchison G Genoogle uses indexing and parallel processing techniques for searching DNA and Proteins sequences. Software for ultra fast local DNA sequence motif search and pairwise alignment for NGS data (FASTA, FASTQ). Global:Global (GG), Global:Local (GL) alignment with statistics Local search with fast k-tuple heuristic, slower but more sensitive than BLAST GPU accelerated Smith Waterman algorithm for multiple shared-host GPUsīLASTX and BLASTP aligner based on double indexingīuchfink B, Xie C, Huson DH, Reuter K, Drost HG Position-specific iterative version CSI-BLAST more sensitive than PSI-BLAST Sequence-context specific BLAST, more sensitive than BLAST, FASTA, and SSEARCH. īurdyshaw CE, Sawyer S, Horton MD, Brook RG, Rekapalli B Distributed with the latest version of BLAST, this wrapper facilitates parallelization of the algorithm on modern hybrid architectures with many nodes and many cores within each node. NCBI compliant multinode and multicore BLAST wrapper.
Local search with fast k-tuple heuristic (Basic Local Alignment Search Tool)Īltschul SF, Gish W, Miller W, Myers EW, Lipman DJ See structural alignment software for structural alignment of proteins. This list of sequence alignment software is a compilation of software tools and web portals used in pairwise sequence alignment and multiple sequence alignment.
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