Search Results for "alignment" - Page 19
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Showing 522 open source projects for "alignment"
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MSA2SNP is a tool for mining SNP sites in multiple sequence alignment (MSA). This tool inherits the easy-to-use interface from MEGA4 Explorer with advance data presentation. MSA2SNP lets you visualize alignments and import from CLUSTAL program directly.
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Tangerine is a protein sequence alignment tool based on cross-correlation. Its aim is to provide maximum sensitivity while being computationally efficient.
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3D Genome Tuner draws circular genome map and enables viewing multi-genomes in 3D context. It also provides genome analysis and sequence alignment, making it a powerful tool in genome studies and demonstrations.
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A peak caller for ChIP-Seq experiments that robustly handles short reads with *multiple* possible mappings. Releases are hosted here, but development source code is available at https://github.com/jakebiesinger/AREM. A Google group has been set up to help with questions from the community and for announcements of new builds. http://groups.google.com/group/arem-announcements
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BoulderALE is an RNA alignment editor, which allows for the annotation of basepairs, annotation and collapsing of features (horizontal) and sequences (vertical), along with 2D display of sequences and base composition given a secondary structure.
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This software is developed by Kalidas (http://openwetware.org/wiki/Kalidas_Y) as part of his Ph.D. thesis. The method enables alignment of ligand molecules considered molecular graphs. It is useful in the domain of drug discovery and bioinformatics.
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Ordered Bijective Interpolated Warping (OBI-Warp) aligns matrices using Dynamic Time Warping with a one-to-one (bijective) smooth warp-function. It is ideal for the chromatographic alignment of complex mass spectrometry proteomics data.
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C++ library for protein sequence profile to profile alignment. Implementing numerous known alignment variants in a flexible and manageable architecture.
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Text2Genome is a set of scripts to extract nucleotide sequences from scientific articles and to map them to genomes and genes using a local alignment algorithm (BLAST/BLAT)
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The DNA Sequence Read Toolkit is a set of programs to convert data from DNA sequencing instruments into formats suitable for archiving, viewing or for onward processing (for example alignment or assembly).
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The CMASA (Contact MAtrix based local Structural Alignment algorithm) were used in detecting local protein structural similarity. And it can be applied to enzyme catalytic site annotation. Also visit: http://159.226.149.45/other1/CMASA/CMASA.htm
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Image and video acquisition for scientific applications, particularly in behavioral biology and neuroscience
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GGredit is library that implements base functionality for a generic graphic editor. DDraw is a diagram editor designed for Gnome that use GGredit. DDraw is inspired to DIA, it can be used to draw many different kinds of diagrams.
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Whole-genome scale multiple genome local alignment search program. Supports unlimited length gapped-seed patterns, parallelization through distributed hashing, and unique a TF-IDF based repeat filtering method.
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BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC. Annotates the locations of conserved elements in multiple sequence while correcting for alignment uncertainty and error.
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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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sigMan is a utility for the analysis of time-dependent signals, especially electropherogram/chromatogram data. It is no longer being actively updated or maintained by me (Nathan Cermak) as of January 2011, for lack of any users.
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Optical ray tracing library based on MATLAB environment Now working on the simple raytracing simulation. Documents are not ready yet. NEW UPDATE : ray generation function, other bug fix and multiple ray treatment
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GOALS is a very flexible, adaptable and powerful tool for prototyping and/or building ontology alignment systems. Reusability of existing matching techniques is encouraged. More details at http://www.dei.isep.ipp.pt/~pmaio/goals.
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Sanchay is a collection of tools and APIs for language researchers. It has some implementations of NLP algorithms, some flexible APIs, several user friendly annotation interfaces and Sanchay Query Language for language resources.
