scholarly journals ASAP: automated sequence annotation pipeline for web-based updating of sequence information with a local dynamic database

2003 ◽  
Vol 19 (5) ◽  
pp. 675-676 ◽  
Author(s):  
A. Kossenkov ◽  
F. J. Manion ◽  
E. Korotkov ◽  
T. D. Moloshok ◽  
M. F. Ochs
Keyword(s):  
Sequence Information ◽  
Local Dynamic ◽  
Sequence Annotation ◽  
Web Based ◽  
Annotation Pipeline

scholarly journals Protein Sequence Annotation Tool (PSAT): a centralized web-based meta-server for high-throughput sequence annotations

2016 ◽  
Vol 17 (1) ◽  
Author(s):  
Elo Leung ◽  
Amy Huang ◽  
Eithon Cadag ◽  
Aldrin Montana ◽  
Jan Lorenz Soliman ◽  
...  
Keyword(s):  
High Throughput ◽  
Protein Sequence ◽  
Sequence Annotation ◽  
Annotation Tool ◽  
Web Based

scholarly journals Genescript: DNA sequence annotation pipeline

2003 ◽  
Vol 19 (9) ◽  
pp. 1177-1178 ◽  
Author(s):  
A. K. Hudek ◽  
J. Cheung ◽  
A. P. Boright ◽  
S. W. Scherer
Keyword(s):  
Dna Sequence ◽  
Sequence Annotation ◽  
Annotation Pipeline

scholarly journals iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures

2019 ◽  
Vol 36 (1) ◽  
pp. 131-135 ◽  
Author(s):  
Jiyao Wang ◽  
Philippe Youkharibache ◽  
Dachuan Zhang ◽  
Christopher J Lanczycki ◽  
Renata C Geer ◽  
...  
Keyword(s):  
Large Fraction ◽  
3D Structure ◽  
Supplementary Information ◽  
Sequence Annotation ◽  
Web Based ◽  
The Public ◽  
Molecular Features ◽  
Density Maps ◽  
3D Molecular Structure ◽  
3D Representations

Abstract Motivation Build a web-based 3D molecular structure viewer focusing on interactive structural analysis. Results iCn3D (I-see-in-3D) can simultaneously show 3D structure, 2D molecular contacts and 1D protein and nucleotide sequences through an integrated sequence/annotation browser. Pre-defined and arbitrary molecular features can be selected in any of the 1D/2D/3D windows as sets of residues and these selections are synchronized dynamically in all displays. Biological annotations such as protein domains, single nucleotide variations, etc. can be shown as tracks in the 1D sequence/annotation browser. These customized displays can be shared with colleagues or publishers via a simple URL. iCn3D can display structure–structure alignments obtained from NCBI’s VAST+ service. It can also display the alignment of a sequence with a structure as identified by BLAST, and thus relate 3D structure to a large fraction of all known proteins. iCn3D can also display electron density maps or electron microscopy (EM) density maps, and export files for 3D printing. The following example URL exemplifies some of the 1D/2D/3D representations: https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmdbid=1TUP&showanno=1&show2d=1&showsets=1. Availability and implementation iCn3D is freely available to the public. Its source code is available at https://github.com/ncbi/icn3d. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals MCAM: A Database to Accelerate the Identification of Functional Cell Adhesion Molecules

2008 ◽  
Vol 6 ◽  
pp. CIN.S341 ◽  
Author(s):  
Anguraj Sadanandam ◽  
Sudipendra Nath Pal ◽  
Joe Ziskovsky ◽  
Prathibha Hegde ◽  
Rakesh K. Singh
Keyword(s):  
Cell Adhesion ◽  
Adhesion Molecules ◽  
Cell Adhesion Molecules ◽  
Expression Patterns ◽  
Sequence Information ◽  
Web Based ◽  
Hematopoietic Stem ◽  
Tumor Tissues ◽  
Using Data ◽  
High Throughput Experiments

In the post-genomic era, computational identification of cell adhesion molecules (CAMs) becomes important in defining new targets for diagnosis and treatment of various diseases including cancer. Lack of a comprehensive CAM-specific database restricts our ability to identify and characterize novel CAMs. Therefore, we developed a comprehensive mammalian cell adhesion molecule (MCAM) database. The current version is an interactive Web-based database, which provides the resources needed to search mouse, human and rat-specific CAMs and their sequence information and characteristics such as gene functions and virtual gene expression patterns in normal and tumor tissues as well as cell lines. Moreover, the MCAM database can be used for various bioinformatics and biological analyses including identifying CAMs involved in cell-cell interactions and homing of lymphocytes, hematopoietic stem cells and malignant cells to specific organs using data from high-throughput experiments. Furthermore, the database can also be used for training and testing existing transmembrane (TM) topology prediction methods specifically for CAM sequences. The database is freely available online at http://www.app1.unmc.edu/mcam .

scholarly journals iCn3D, a Web-based 3D Viewer for Sharing 1D/2D/3D Representations of Biomolecular Structures

2018 ◽  
Author(s):  
Jiyao Wang ◽  
Philippe Youkharibache ◽  
Dachuan Zhang ◽  
Christopher J. Lanczycki ◽  
Renata C. Geer ◽  
...  
Keyword(s):  
Large Fraction ◽  
3D Structure ◽  
Structure Alignment ◽  
Supplementary Information ◽  
Sequence Annotation ◽  
Web Based ◽  
Link Type ◽  
Molecular Features ◽  
Density Maps ◽  
3D Representations

AbstractSummaryiCn3D (I-see-in-3D) is a web-based 3D molecular structure viewer focusing on the interactive structural analysis. It can simultaneously show 3D structure, 2D molecular contacts, and 1D protein and nucleotide sequences through an integrated sequence/annotation browser. Pre-defined and arbitrary molecular features can be selected in any of the 1D/2D/3D windows as sets of residues and these selections are synchronized dynamically in all displays. Biological annotations such as protein domains, single nucleotide variations, etc. can be shown as tracks in the 1D sequence/annotation browser. These customized displays can be shared with colleagues or publishers via a simple URL. iCn3D can display structure-structure alignment obtained from NCBI’s VAST+ service. It can also display the alignment of a sequence with a structure as identified by BLAST, and thus relate 3D structure to a large fraction of all known proteins. iCn3D can also display electron density maps or electron microscopy (EM) density maps, and export files for 3D printing. The following example URL exemplifies some of the 1D/2D/3D representations: https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmdbid=1TUP&showanno=1&show2d=1&showsets=1.Availability and implementationiCn3D is freely available to the public. Its source code is available at https://github.com/ncbi/icn3d.Supplementary informationUser instructions are available at Bioinformatics online

The PBL-Evaluator: a web-based tool for assessment in tutorials

1998 ◽  
Vol 62 (9) ◽  
pp. 671-674
Author(s):  
JF Chaves ◽  
JA Chaves ◽  
MS Lantz
Keyword(s):  
Web Based

Using Popular Mobile Devices in Voice Therapy

2013 ◽  
Vol 23 (3) ◽  
pp. 82-87 ◽  
Author(s):  
Eva van Leer
Keyword(s):  
Exercise Behavior ◽  
Voice Therapy ◽  
Pure Oxygen ◽  
Mobile Platforms ◽  
Self Monitoring ◽  
Web Based ◽  
Motivational Messages ◽  
Related Information ◽  
Health Related ◽  
Tailored Approach

Mobile tools are increasingly available to help individuals monitor their progress toward health behavior goals. Commonly known commercial products for health and fitness self-monitoring include wearable devices such as the Fitbit© and Nike + Pedometer© that work independently or in conjunction with mobile platforms (e.g., smartphones, media players) as well as web-based interfaces. These tools track and graph exercise behavior, provide motivational messages, offer health-related information, and allow users to share their accomplishments via social media. Approximately 2 million software programs or “apps” have been designed for mobile platforms (Pure Oxygen Mobile, 2013), many of which are health-related. The development of mobile health devices and applications is advancing so quickly that the Food and Drug Administration issued a Guidance statement with the purpose of defining mobile medical applications and describing a tailored approach to their regulation.

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