94,063 research outputs found
Multiple sequence alignment with user-defined constraints at GOBICS
Most multi-alignment methods are fully automated, i.e. they are based on a fixed set of mathematical rules. For various reasons, such methods may fail to produce biologically meaningful alignments. Herein, we describe a semi-automatic approach to multiple sequence alignment where biological expert knowledge can be used to influence the alignment procedure. The user can specify parts of the sequences that are biologically related to each other; our software program uses these sites as anchor points and creates a multiple alignment respecting these user-defined constraints. By using known functionally, structurally or evolutionarily related positions of the input sequences as anchor points, our method can produce alignments that reflect the true biological relationships among the input sequences more accurately than fully automated procedures can do
PROMALS3D web server for accurate multiple protein sequence and structure alignments
Multiple sequence alignments are essential in computational sequence and structural analysis, with applications in homology detection, structure modeling, function prediction and phylogenetic analysis. We report PROMALS3D web server for constructing alignments for multiple protein sequences and/or structures using information from available 3D structures, database homologs and predicted secondary structures. PROMALS3D shows higher alignment accuracy than a number of other advanced methods. Input of PROMALS3D web server can be FASTA format protein sequences, PDB format protein structures and/or user-defined alignment constraints. The output page provides alignments with several formats, including a colored alignment augmented with useful information about sequence grouping, predicted secondary structures and consensus sequences. Intermediate results of sequence and structural database searches are also available. The PROMALS3D web server is available at: http://prodata.swmed.edu/promals3d/
Circulant temporal encoding for video retrieval and temporal alignment
We address the problem of specific video event retrieval. Given a query video
of a specific event, e.g., a concert of Madonna, the goal is to retrieve other
videos of the same event that temporally overlap with the query. Our approach
encodes the frame descriptors of a video to jointly represent their appearance
and temporal order. It exploits the properties of circulant matrices to
efficiently compare the videos in the frequency domain. This offers a
significant gain in complexity and accurately localizes the matching parts of
videos. The descriptors can be compressed in the frequency domain with a
product quantizer adapted to complex numbers. In this case, video retrieval is
performed without decompressing the descriptors. We also consider the temporal
alignment of a set of videos. We exploit the matching confidence and an
estimate of the temporal offset computed for all pairs of videos by our
retrieval approach. Our robust algorithm aligns the videos on a global timeline
by maximizing the set of temporally consistent matches. The global temporal
alignment enables synchronous playback of the videos of a given scene
Calipso: Physics-based Image and Video Editing through CAD Model Proxies
We present Calipso, an interactive method for editing images and videos in a
physically-coherent manner. Our main idea is to realize physics-based
manipulations by running a full physics simulation on proxy geometries given by
non-rigidly aligned CAD models. Running these simulations allows us to apply
new, unseen forces to move or deform selected objects, change physical
parameters such as mass or elasticity, or even add entire new objects that
interact with the rest of the underlying scene. In Calipso, the user makes
edits directly in 3D; these edits are processed by the simulation and then
transfered to the target 2D content using shape-to-image correspondences in a
photo-realistic rendering process. To align the CAD models, we introduce an
efficient CAD-to-image alignment procedure that jointly minimizes for rigid and
non-rigid alignment while preserving the high-level structure of the input
shape. Moreover, the user can choose to exploit image flow to estimate scene
motion, producing coherent physical behavior with ambient dynamics. We
demonstrate Calipso's physics-based editing on a wide range of examples
producing myriad physical behavior while preserving geometric and visual
consistency.Comment: 11 page
EvolveAGene 3: A DNA coding sequence evolution simulation program
EvolveAGene 3 is a realistic coding sequence simulation program that separates mutation from selection and allows the user to set selection conditions, including variable regions of selection intensity within the sequence and variation in intensity of selection over branches. Variation includes base substitutions, insertions and deletions. Output includes a log file, the true tree and both unaligned coding sequence and protein sequences and the true DNA and protein alignments
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