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At least 1,351 records · Page 75Linked to original sources
PubMed2002

CINEMA-MX: a modular multiple alignment editor.

UNLABELLED: Analyzing and visualizing multiple sequence alignments is a common task in many areas of molecular biology and bioinformatics. Many tools exist for this purpose, but are not easily customizable for specific in-house uses. Here we report the development of an editor, CINEMA-MX, that addresses these issues. CINEMA-MX is highly modular and configurable, and we present examples to illustrate its extensibility. AVAILABILITY: The program and full source code, which are available from http://www.bioinf.man.ac.uk/dbbrowser/cinema-mx, are being released under a combination of the LGPL and GPL, for Unix or Windows platforms.

Computer Graphics↗
PubMed2003

Matrix2png: a utility for visualizing matrix data.

UNLABELLED: We describe a simple software tool, 'matrix2png', for creating color images of matrix data. Originally designed with the display of microarray data sets in mind, it is a general tool that can be used to make simple visualizations of matrices for use in figures, web pages, slide presentations and the like. It can also be used to generate images 'on the fly' in web applications. Both continuous-valued and discrete-valued (categorical) data sets can be displayed. Many options are available to the user, including the colors used, the display of row and column labels, and scale bars. In this note we describe some of matrix2png's features and describe some places it has been useful in the authors' work. AVAILABILITY: A simple web interface is available, and Unix binaries are available from http://microarray.cpmc.columbia.edu/matrix2png. Source code is available on request.

Color↗
PubMed2003

BioEditor-simplifying macromolecular structure annotation.

SUMMARY: BioEditor is an application to enable scientists and educators to prepare and present structure annotations containing formatted text, graphics, sequence data, and interactive molecular views. It is intended to bridge the gap between printed journal articles and Internet presentation formats. BioEditor is relevant in the era of structural genomics, where annotation and publication could become the rate determining step in structure determination. AVAILABILITY: BioEditor is available at http://bioeditor.sdsc.edu. The Web site includes the latest version of the software for Microsoft Windows, including documentation, the opportunity to submit bug reports and suggestions, example documentaries prepared with BioEditor and a repository where users can submit documentaries for posting to the site.

Biopolymers↗
PubMed2004

The Jalview Java alignment editor.

Multiple sequence alignment remains a crucial method for understanding the function of groups of related nucleic acid and protein sequences. However, it is known that automatic multiple sequence alignments can often be improved by manual editing. Therefore, tools are needed to view and edit multiple sequence alignments. Due to growth in the sequence databases, multiple sequence alignments can often be large and difficult to view efficiently. The Jalview Java alignment editor is presented here, which enables fast viewing and editing of large multiple sequence alignments.

Algorithms↗
PubMed2004

CAAT-Box, Contigs-Assembly and Annotation Tool-Box for genome sequencing projects.

MOTIVATION: Contigs-Assembly and Annotation Tool-Box (CAAT-Box) is a software package developed for the computational part of a genome project where the sequence is obtained by a shotgun strategy. CAAT-Box contains new tools to predict links between contigs by using similarity searches with other whole genome sequences. Most importantly, it allows annotation of a genome to commence during the finishing phase using a gene-oriented strategy. For this purpose, CAAT-Box creates an Individual Protein file (IPF) for each ORF of an assembly. The nucleotide sequence reported in an IPF corresponds to the sequence of the ORF with 500 additional bases before the ORF and 200 bases after. For annotation, additional information like Blast results can be added or linked to the IPFs as well as automatic and/or manual annotations. When a new assembly is performed, CAAT-Box creates new IPFs according to the old IPF panel. CAAT-Box recognizes the modified IPFs which are the only ones used for a new automatic analysis after each assembly. Using this strategy, the user works with a group of IPFs independently of the closure phase progression. The IPFs are accessible by a web server and can therefore be modified and commented by different groups. RESULT: CAAT-Box was used to obtain and to annotate several complete genomes like Listeria monocytogenes or Streptococcus agalactiae. AVAILABILITY: The program may be obtained from the authors and is freely available to non-profit organisations.

Algorithms↗
PubMed2004

Drawing phylogenetic trees in LATEX and Microsoft Word.

UNLABELLED: newicktree is a PSTricks-based LATEX package which enables phylogenetic trees described in the Newick format to be drawn directly into LATEX documents. mswordtree is a macro for producing phylogenetic trees using the drawing elements available in Microsoft Word. AVAILABILITY: Both programs are available free from the John Innes Centre's Bioinformatics Research Group website at http://jic-bioinfo.bbsrc.ac.uk/bioinformatics-research/software/index.html. SUPPLEMENTARY INFORMATION: A full user-guide for newicktree and installation and usage instructions for mswordtree and available at http://jic-bioinfo.bbsrc.ac.uk/bioinformatics-research/software/index.html

Computer Graphics↗
PubMed2004

RALEE--RNA ALignment editor in Emacs.

UNLABELLED: Production of high quality multiple sequence alignments of structured RNAs relies on an iterative combination of manual editing and structure prediction. An essential feature of an RNA alignment editor is the facility to mark-up the alignment based on how it matches a given secondary structure prediction, but few available alignment editors offer such a feature. The RALEE (RNA ALignment Editor in Emacs) tool provides a simple environment for RNA multiple sequence alignment editing, including structure-specific colour schemes, utilizing helper applications for structure prediction and many more conventional editing functions. This is accomplished by extending the commonly used text editor, Emacs, which is available for Linux, most UNIX systems, Windows and Mac OS. AVAILABILITY: The ELISP source code for RALEE is freely available from http://www.sanger.ac.uk/Users/sgj/ralee/ along with documentation and examples. CONTACT: sgj@sanger.ac.uk

Algorithms↗
PubMed2006

Phase coupling in a cerebro-cerebellar network at 8-13 Hz during reading.

Words forming a continuous story were presented to 9 subjects at frequencies ranging from 5 to 30 Hz, determined individually to render comprehension easy, effortful, or practically impossible. We identified a left-hemisphere neural network sensitive to reading performance directly from the time courses of activation in the brain, derived from magnetoencephalography data. Regardless of the stimulus rate, communication within the long-range neural network occurred at a frequency of 8-13 Hz. Our coherence-based detection of interconnected nodes reproduced several brain regions that have been previously reported as active in reading tasks, based on traditional contrast estimates. Intriguingly, the face motor cortex and the cerebellum, typically associated with speech production, and the orbitofrontal cortex, linked to visual recognition and working memory, additionally emerged as densely connected components of the network. The left inferior occipitotemporal cortex, involved in early letter-string or word-specific processing, and the cerebellum turned out to be the main forward driving nodes of the network. Synchronization within a subset of nodes formed by the left occipitotemporal, the left superior temporal, and orbitofrontal cortex was increased with the subjects' effort to comprehend the text. Our results link long-range neural synchronization and directionality with cognitive performance.

Adult↗
PubMed2000

Morphographic analysis as a word identification strategy for deaf readers.

This review of theoretical and research literature develops a rationale for morphographic analysis as a principal component of instruction on word identification for deaf students. The word identification process is conceptualized with regard to visually accessible morphographic components of text, including definition of the variables involved in morphographic analysis. Evidence accumulated from varied sources is presented to support this rationale for another approach to reading with deaf students. The conclusion outlines implications for instructional intervention and for future research.

Journal Article↗
PubMed2003

Vocabulary Assessment of Deaf and Hard-of-Hearing Children From Infancy Through the Preschool Years.

The purpose of this article is to inform researchers and practitioners about potential challenges in the selection, administration, and interpretation of results of measures of vocabulary assessment when working with deaf and hard-of-hearing children. This article reviews methods that can be used to assess vocabulary of children through the age of 5 years, including naturalistic observation, parent report measures, and standardized vocabulary tests. The authors also describe procedures to assess word-learning processes available to children to facilitate vocabulary acquisition. General cautions regarding the use of assessment tools with deaf and hard-of-hearing children are reviewed, as well as cautions for specific assessment measures. Finally, based on available research, suggestions are offered regarding what each assessment test can tell us about deaf and hard-of-hearing children's vocabulary development.

Journal Article↗
PubMedDate not supplied

Practical computer applications for endoscopy.

A computer can facilitate a nurse's administrative tasks, resulting in increased time to spend with patients. Data can easily be organized and retrieved. Forms can be created when there is no ready-made form at hand. Document revision is easy and cost-effective because the form is not typeset until it has been tried and is ready for permanent adoption. The outcome will be a nursing practice that is more efficient, effective, and professionally rewarding.

Database Management Systems↗
PubMed1997

Brain potentials indicate differences between regular and irregular German plurals.

Event-related brain potentials were recorded as 18 German-speaking subjects read sentences that contained as critical words German nouns in correct and incorrect plural forms. Two types of plurals were investigated: regular -s plurals (e.g. Karussell-s 'roundabouts') and irregular -(e)n plurals (Muskel-n "muscles'). We compared correct regular and irregular plurals with incorrect ones; the latter had -(e)n on nouns that actually take -s plurals (*Karussell-en), or -s on nouns that require -(e)n (*Muskel-s). ERPs showed different responses to regular and irregular plurals: incorrect irregular plurals (*Muskel-s) elicited a ramp-shaped left frontotemporal negativity, whereas incorrect regulars (*Karussell-en) produced a central phasic negativity with a maximum at 380 ms. This dissociation supports the view that regularly inflected words are processed differently from irregularly inflected ones.

Adult↗
PubMed1996

A procedure for testing speech intelligibility in a virtual listening environment.

OBJECTIVE: The development of a test of virtual speech intelligibility in noise that enables assessment in typical, everyday listening situations. To eliminate extraneous confounding factors, digital signal processing was incorporated to simulate listening environments and source locations and allow presentation of stimuli via earphones. DESIGN: Source-to-eardrum transfer functions measured on KEMAR for various source locations in anechoic and reverberant environments were used to process monosyllabic words and speech-spectrum noise. Speech intelligibility was measured for three speech and noise configurations in two environments using an adaptive procedure to determine the signal-to-noise (S/N) ratio for 50% intelligibility. RESULTS: Normal-hearing listeners achieved 50% intelligibility of monosyllabic words at significantly lower S/N ratios in a virtual anechoic environment than in a virtual reverberant environment. Speech intelligibility improved significantly in both environments when the speech and noise sources were separated, but the intelligibility gain in the anechoic environment was four times larger than in the reverberant environment. CONCLUSIONS: This test is easy to administer and score, and it provides a means for measuring: 1) the effects of separating speech and noise sources and 2) the effects of reverberation on speech intelligibility in noise while eliminating confounding factors such as calibration.

Hearing↗