Search Results for "display"

"I see in 3D" (iCn3D) Structure Viewer is not only a web-based 3D viewer, but also a structure analysis tool interactively or in the batch mode using NodeJS scripts based on the npm package icn3d. iCn3D synchronizes the display of 3D structure, 2D interaction, and 1D sequences and annotations. Users' custom displays can be saved in a short URL or a PNG image. The complete package of iCn3D including Three.js and jQuery is in the directory "dist" after you get the source code with the "Code" button. View a 3D structure in iCn3D, input a PDB ID, and click "Load". ...

Over 1,000,000 page views per month. Jmol/JSmol is a molecular viewer for 3D chemical structures that runs in four independent modes: an HTML5-only web application utilizing jQuery, a Java applet, a stand-alone Java program (Jmol.jar), and a "headless" server-side component (JmolData.jar). Jmol can read many file types, including PDB, CIF, SDF, MOL, PyMOL PSE files, and Spartan files, as well as output from Gaussian, GAMESS, MOPAC, VASP, CRYSTAL, CASTEP, QuantumEspresso, VMD, and many other...

XLibraryDisplay is an intuitive sequence analysis program optimized for protein engineering. It is ideal for all directed evolution platforms including phage, ribosome, and yeast display. Analysis can be quickly done on hundreds to thousands of sequences. Best suited for Sanger sequencing. Requirements: Microsoft Windows XP, 7, 8, or 10 and Excel 2007, 2010, 2013, or 2016 Described in Stafford et al JCIM 2014: http://pubs.acs.org/doi/abs/10.1021/ci500362s

The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments for bacterial and archaeal 16S rRNA sequences, fungal LSU and fungal ITS sequences, with confidence estimates for each assignment. More information and tutorials on how to install, use and retrain RDP Clasifier can be found on at https://github.com/rdpstaff/classifier and John Quensen's blog (https://john-quensen.com/). Citation: 1. Wang Q, Garrity GM, Tiedje JM, Cole JR....

bruread is a program to read and display NMR data in the Bruker XWIN-NMR format. The program has a command-line interface and a graphic display based on gnuplot. - Note that this is only an NMR spectrum *viewer*, not a full-fledged data evaluation suite

...The unique functionality in NicheA, not available in other software programs, is estimating Grinnellian niches of species based on environmental variables and occurrence records, but with a clear focus on fundamental ecological niches. NicheA can display ecological niches; calculate their shape, density, location, and other attributes; and quantify similarity among multiple niches.

A Mass Difference Calculator with a graph for MassLynx. Bring in a text file with reference masses and then paste in or browse in another file with a list of mass/intensity pairs. Then look at the best matching points and see what the difference between reference and data comes out as. This is a companion app to ResCalc3

These scripts written in java can be used for deep sequencing analysis of the scFv antibodies from a synthetic antibody library and yields complete sequence information on the randomized areas of antibodies enriched from the library by phage display. The methods are descriped in Lövgen, J., Pursiheimo, J.P., Pyykkö, M., Salmi, J. & Lamminmäki, U. (2016) Next generation sequencing of all variable loops of synthetic single framework scFv – application in anti-HDL antibody selections. New Biotechnology 33:790-796.

Gene Slider can be used to visualize conservation and entropy of aligned DNA and protein sequences by presenting them as one long sequence logo. The presented sequence logo can be zoomed in and out. It can also display motifs in alignments. A built-in search function can be used to find motifs. Gene Slider is available online on the Bio-Analytic Resource and for download here.

iMet-Q (intelligent Metabolomic Quantitation) is an automated tool with friendly user interfaces for quantifying metabolites in full-scan liquid chromatography-mass spectrometry (LC-MS) data. It has a complete quantitation procedure for noise removal, peak detection and peak alignment. In addition to accurate quantitation, iMet-Q provides the charge states and isotope ratios of detected compounds. It accepts input data in netCDF, mzXML, and mzML format and exports quantitation results in csv...

TopiaryExplorer has moved to GitHub. Find the new project info page here: https://github.com/qiime/Topiary-Explorer. If you need help or would like to add a bug/feature request, please do so there.

3D viewer which arranges BLAST hits and other bioinformatics-related alignments in a rotating, cylindrical display. Feedback appreciated. NOTE: requires Java3d installation. Superceded by Cylindrical Alignment App

...The resolution can be optionally compared to a threshold you specify and the result is displayed as Pass/Fail using a tick or cross alongside the resolution. You can choose to display a graph which shows the position and threshold result overlaid on the data. The resolution result can be printed and or copied into the clipboard so you can paste it into a report of your own.

To overcome current limitations in published MS data accessibility, we introduce a browser-based spectrum viewer that aims to allow exploration of alternative interpretations for MS spectra and additionally: can be operated by non-specialists, is open source, can be integrated into other software, gives appropriate publication-quality output. Spectrum Viewer is implemented totally on the client side using XHTML for menus and dialogs, SVG for spectrum and peptide display, and Javascript to drive functionality. It comprises 3 parts: (1) the core Spectrum Viewer displays peptide-spectrum matches and implements zooming, mouse-over peaks to highlight matching parts of peptide, mouse-over parts of peptide to highlight matching peaks, export SVG, and API; (2) the Auxiliary Annotator matches peptide to spectrum for given parameters and prepares the data for the Viewer; (3) these reside on a web page that provides the user control over peptides, spectra and other parameters e.g. linker mass.

...The program aims to allow the identification of regions where the values of either the CN state or the LOH scores are the same in all the affected individuals, but none of the unaffected individuals have the same value. As well as visualising the CN state and LOH data, the program will also display Log(2) ratio, smooth signal and allele difference values that may also be obtained from the Affymetrix SNP 6.0 array (details on how to export the data are here). CN state, Log(2) ratio and the smooth signal data may be derived from either the SNP or CNV probes on the SNP microarray chip, where as the LOH and allele difference values are derived solely from the SNP probes.

A set of command-line utilities for annotating and manipulating DNA sequences in FASTA format. Generate restriction fragments, ORF's, translations, reverse complement, etc. . - and tie it all together with Unix pipes for complete virtual cloning.

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.

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.

IDEA (Interactive Display for Evolutionary Analyses) augments PAML with a graphical interface, phylogeny reconstruction using PhyML or PHYLIP, convenient and efficient parallel processing and visualizations.

A Java application used in whole genome analysis to display SNPs in a genomic context. Supplementary data is downloaded from various public data sources on the fly and saved locally in a cache. Custom data can be added as supplementary tracks.

The goal of Picklist Editor is to display and modify pick lists before spot picking (in proteomics).

JAMBLAST: Java Application Manager for the ncbi BLAST results. It is a graphic application that allow the user to display, filter, sort, import/export, store/manage BLAST results produced with the NOBLAST (https://sourceforge.net/projects/noblast).

APoDIx is a Portable Bio-Database Index system. It retrieves biological database information from the website of Oxford Journals, save them in a local position, and provides a viewer for display and search the information.

Geneview is a visualisation tool to display genetic sequence data stored in nucleic sequence databases like <A HREF="http://www.ncbi.nlm.nih.gov/Genbank/">GenBank</A>.

JPhylo is a Java based visualization program used to display sequences of phylogenetic trees.