Search Results for "smith waterman opal"

...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

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...

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.

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/

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/

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.

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.

Smith-Waterman algorithm implementation on CPU, GPU and FPGA.

Multi-functional batch sequence aligner incorporating Needleman-Wunsch, Smith-Waterman and Oommen-Kashyap algorithms along with compound alignment of secondary sequences.

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.

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.

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.

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