Search Results for "ids"

...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". You can also click the "File" menu to "Open File" or input other IDs. You can open a browser in your Virtual Reality (VR) headset and view a 3D structure in iCn3D. Then click the button "Enter VR" at the bottom center of your browser to enter the VR view. You can select residues with the trigger button.

To select miRNA target genes we developed software in MATLAB® (MathWorks®) called miRDiana that collects the union of mouse validated targets from the TargetScan, MicroCosm, mirTarBase and miRWalk 2.0 databases. Firstly, the software downloads each database and preprocesses by standardizing the miRNA and gene names. It strips the miRNA names from the species ids and converts the gene names to the official symbols of the National Center for Biotechnology Information (NCBI) database. Next, for each potential gene target it calculates an incidence matrix with all the miRNAs of each database targeting such gene. Finally, it builds a consensus matrix with the cases of the appearance of each miRNA in the four analyzed miRNA databases.

A command-line utility to manipulate biological sequences from a FASTA or FASTQ file. It can, given a list of identifiers, get only a subset of the sequences (or their complement, i.e., sequences NOT in the list). Can also get sequence number N only. Compressed sequences files are supported if readable by zcat.

Drug name recognition and normalisation/grounding to DrugBank ids and standard names. Package provides 2 taggers: 1. DrugTagger - CRF-based with DrugBank presence feature (see feature set for details). 2. DrugnameGazetteer - gazetteer/dictionary-based. Dictionary created from DrugBank.ca database. Both taggers include grounding/normalisation to DrugBank ids and standard names. Feature set: Word, Word-1, Word+1, Word-1_Word, Word_Word+1, DrugBankPresence, POS DrugBankPresence feature indicates the presence of the drug name in the DrugBank. ...

PROMPT is a system for retrieval, analysis, mapping and comparison of proteins. It allows easy mapping of different types of sequence IDs, data retrieval and integration, a multitude of analysis and comparison algorithms and a full-blown easy to use GUI.