Search Results for "smith waterman"
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Showing 20 open source projects for "smith waterman"
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CUDASW++: Smith-Waterman Algorithm
The fastest Smith-Waterman protein database search algorithm on GPUs
CUDASW++ software is a public open source software for Smith-Waterman protein database searches on Graphics Processing Units with CUDA. This software have been added to the NVIDIA Tesla Bio Workbench (http://www.nvidia.com/object/swplusplus_on_tesla.html -
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adapter trimmer
We implement a very simple approach. Each read is searched for the jun
...If a match to either side of the junction is found then the entire 38bp juncton is clipped. This means the algorithm can tolerate an indel error in one of the sides of the junction, but not both. Optionally Smith-Waterman alignment can be turned on with -w which resolves this issue, although the code is less tested. eg. this will be caught: CTGTCTCT-TA-TACACATCTAGATGTGTATAAGAGACAG but not this: CTGTCTCT-TA-TACACATCTAGATGT-GTATAAGAGACAG -
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SW#
smith waterman, gpu, cuda, alignment
SW# (swsharp) is a library for sequence alignment based on CUDA enabled GPUs. It utilizes Hirschbergs and Ukkonens algorithm for memory efficiency and additional speed up. The library is scalable for use with multiple GPUs. Some parts of the library utilize MPI for CUDA enabled clusters. This work has been supported in part by Croatian Science Foundation under the project UIP-11-2013-7353. Database search now... -
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BABA stands for Basic-Algorithms-of-Bioinformatics Applet. This project aims to create a set of bioinformatic algorithms presented didactically. The algorithms available at the moment are: Needleman&Wunsch, Smith&Waterman, Four Russians and Nussinov.
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SWAPHI: Smith-Waterman on Intel Xeon Phi
The first protein sequence database search on shared-host Xeon Phis
The first parallel algorithm to accelerate the Smith-Waterman protein database search on shared-host multiple Intel Xeon Phi coprocessors. By searching against the UniProtKB/TrEMBL database, SWAPHI achieves a performance of up to 58.8 billion cell updates per second (GCUPS) on a single Xeon Phi and up to 228.4 GCUPS on four Xeon Phis. -
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SWAPHI-LS: Alignment on Xeon Phi Cluster
Smith-Waterman long DNA sequence alignment on Xeon Phi clusters
The first parallel Smith-Waterman algorithm exploiting Intel Xeon Phi clusters to accelerate the alignment of long DNA sequences. This algorithm is written in C++ (with a set of SIMD intrinsic extensions), OpenMP and MPI. The performance evaluation revealed that our algorithm achieves very stable performance, and yields a performance of up to 30.1 GCUPS on a single Xeon Phi and up to 111.4 GCUPS on four Xeon Phis sharing a host. -
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CUDAlign
CUDAlign is a tool that aligns huge DNA sequences in CUDA capable GPUs
CUDAlign is a tool able to align pairwise DNA sequences of unrestricted size in CUDA GPUs, using the Smith-Waterman algorithm combined with Myers-Miller. It produces the optimal alignment of 1 million base sequences in 45 seconds using a GTX 560 Ti. Many optimizations are being developed for this software. Look at the following papers for detailed information: [1] Edans Sandes, Alba Melo. Retrieving Smith-Waterman Alignments with Optimizations for Megabase Biological Sequences using GPU. ... -
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...The given sequences are aligned by Sequence Alignment methodology - arranging sequences of DNA, RNA, protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. The sequence Alignment is done by using The Smith-waterman algorithm - a general local alignment method also based on dynamic programming. In this project user has an option to save sequence in either of these formats. FASTA format or CLUSTAL format.Medical Fields can make use of this application .
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NeedlemanWunsch
Fast global sequence alignment for the masses!
MOVED TO GITHUB: https://github.com/noporpoise/seq-align Global optimal sequence alignment using the Needleman-Wunsch algorithm. Aligns DNA, RNA, protein sequence and more! See our sister project local alignment using Smith-Waterman: http://sourceforge.net/projects/smithwaterman/ -
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Swift Sequence Alignment Program
GPU-based DNA sequence alignment program using Smith-Waterman
Swift is a DNA sequence alignment program that produces gapped alignment using the Smith-Waterman algorithm. It takes in a query file (FASTA format) and a reference file (FASTA format) as input. It outputs the reference name, read name, gapped alignment, alignment score, alignment start and end positions, and alignment length. I gave a talk on Swift in the GPU Technology Conference 2012. The talk can be accessed at http://www.gputechconf.com/gtcnew/on-demand-GTC.php?... -
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SmithWaterman
Fast local sequence alignment for the masses!
MOVED TO GITHUB: https://github.com/noporpoise/seq-align An implementation of the Smith-Waterman local sequence alignment algorithm. See our sister project global alignment using Needleman-Wunsch: http://sourceforge.net/projects/needlemanwunsch/ -
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JFinisher
JFinisher is software for alignment, editing and manipulation DNA seqs
JFinisher is software for alignment, editing and manipulation of biological sequences. It aims to assist in the finishing of genome assembly. Starting from a reference sequence, the program align contigs using Smith-Waterman local alignment algoritm with auxiliary methods, allowing management of the alignments generated. It has graphical interface for manipulation and visualization of the actions, uniting features that help in editing the sequences. It has internal projects manageable and ability to export results in the standard formats of the area. -
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A log anomaly detector tool which uses a modified Smith Waterman algorithm to identify matching (or non-matching) messages, against archived syslog messages in real time.
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Multi-functional batch sequence aligner incorporating Needleman-Wunsch, Smith-Waterman and Oommen-Kashyap algorithms along with compound alignment of secondary sequences.
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An efficient implementation of the Smith-Waterman algorithm that takes advantage of SIMD instruction sets in modern CPUs. The Smith-Waterman algorithm is used for sequence alignment in bioinformatics.
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JAligner is an open source Java implementation of the dynamic programming algorithm Smith-Waterman with Gotoh's improvement for biological local pairwise sequence alignment with the affine gap penalty model.
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NeoBio is a Java class library of Computational Biology Algorithms. The current version consists mainly of pairwise sequence alignment algorithms such as the classical dynamic programming methods of Needleman-Wunsch and Smith-Waterman.
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Bioinformatics program for analysing two (currently) or more (in the future) protein sequences and compare them using a Smith-Waterman and/or Needleman-Wunsch algorithms. Also set on gathering inherent statistical analysis from the process and displaying
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