Search PubMed⌕ Search
Home/Archive/PubMed

PubMed · 9852962

CINEMA--a novel colour INteractive editor for multiple alignments.

D J Parry-Smith·A W Payne·A D Michie·T K Attwood
View original source ↗Export metadata ↓

Abstract

CINEMA is a new editor for manipulating and generating multiple sequence alignments. The program provides both an interface to existing databases of alignments on the Internet and a tool for constructing and modifying alignments locally. It is written in Java, so executable code will run on most major desktop platforms without modification. The implementation is highly flexible, so the applet can be easily customised with additional functions; and the object classes are reusable, promoting rapid development of program extensions. Formerly, such extended functionality might have been provided via browser plug-ins, which have to be downloaded and installed on every client before loading data. Now, for the first time, an applet is available that allows interactive client-side processing of an alignment, which can then be stored or processed automatically on the server. The program is embedded in a comprehensive help file and is accessible both as a stand-alone tool on UCL's Bioinformatics Server; http:/(/)www.biochem.ucl.ac.uk/bsm/dbbrowser+ ++/CINEMA2.02/, and as an integral part of the PRINTS protein fingerprint database. Exploitation of such novel technologies revolutionises the way users may interact with public databases in the future: bioinformatics centres need not simply provide data, but are now able to offer the means by which information is visualised and manipulated, without the requirement for users to install software.

Explore related subjects

Color PerceptionComputational BiologyImage Processing, Computer-AssistedInternetSequence AlignmentSoftwareJournal ArticleResearch Support, Non-U.S. Gov't

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

D J Parry-Smith, A W Payne, A D Michie, T K Attwood. 1998-10-09. CINEMA--a novel colour INteractive editor for multiple alignments.. https://doi.org/10.1016/s0378-1119(97)00650-1

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2006

Discrete color filling beyond luminance gaps along perceptual surfaces.

Perceived color at a point in space is not determined simply by the color directly stimulating the corresponding retinal position. Surface color is informed by flanking edge signals, which also serve to inhibit the intrusion of signals from neighboring surfaces. Spatially continuous local interactions among color and luminance signals have been implicated in a propagation process often referred to as filling-in. Here, we report a phenomenon of discrete color filling whereby color jumps over luminance gaps filling into disconnected regions of the stimulus. This color filling is found to be blocked at boundaries defined by texture. The color filling is also highly specific to the elements belonging to a common perceptual surface, even when multiple surfaces are transparently overlaid. Our results indicate that color filling can be governed by a host of visual cues outside the realm of first-order color and brightness, via their impact on perceptual surface segmentation and segregation.

Color Perception↗
PubMed2006

Combining local and global contributions to perceived colour: an analysis of the variability in symmetric and asymmetric colour matching.

Are surfaces' colours judged from weighted averages of the light that they reflect to the eyes and the colour contrast at their borders? To find out we asked subjects to set the colour and luminance of test disks to match reference disks, on various backgrounds, and analysed the variability in their settings. Most of the variability between repeated settings was in luminance. The standard deviations in the set colour were smallest when the disk and background were the same colour, irrespective of the colour itself. Matches were equally precise for greenish or reddish disks on a grey background, as for grey disks on a greenish or reddish background. The precision was less dependent on the colour contrast at the disks' borders when the backgrounds were more complex and when there was a large luminance contrast at the disks' borders. Subjects were less precise when different colours surrounded the two disks. These findings are consistent with the perceived colour at any position being a weighted average of the local cone excitation ratio and the change in the cone excitation ratio at the borders of the surface in question. However, the involved weights must be variable and depend systematically on parameters such as the luminance contrast at the surface's borders and other chromatic contrasts within the scene.

Color Perception↗
PubMed2006

Modularity beyond perception: evidence from single task interference paradigms.

We combine the Dimension-Action (DA) model with translational models to account for both the Stroop and the flanker effects. The basic assumption of the model is that there are distinct visual modules, each of which is endowed with both perception and response selection processes. We contrast this model with an alternative widespread view, the standard view, according to which the same response selection processes are shared by all tasks. The two views have different predictions concerning the flanker and Stroop tasks. Seven experiments test these predictions. The first five experiments show that there is a fundamental difference between the typical Stroop and flanker effects. Moreover, these experiments show that words denoting colors can affect print colors only when they are required for naming or when participants verbally mediate the print color task. Experiments 6 and 7 show that an analogous interaction between color and shape exists in the flanker task. These experiments as well as previous studies are consistent with the DA model and the modular view and pose serious difficulties for the standard view. Wider implications of a visual modular architecture are discussed as well.

Color Perception↗