Atom Biology General Molecule Reaction Tools Trial Virus

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Ketcher File Structure for Reaction
What is the Ketcher file structure for a chemical reaction? The Ketcher file structure for a chemical reaction is an extension of the Ketcher file structure for a molecule. Additional molecule objects are added as reactants, reagents, solvents, and products of the reaction. A long arrow is also adde... 2024-02-18, 1003🔥, 0💬

Read Sequence Alignments with Bio.AlignIO
How to Read Sequence Alignments with Bio.AlignIO package? Bio.AlignIO module allows you to read and write Sequence Alignments as MultipleSeqAlignment objects. Enter the following sequence alignment file, PF05371_seed.faa, in FASTA format. &gt;COATB_BPIKE/30-81 AEPNAATNYATEAMDSLKTQAIDLISQTWP VVTTV... 2023-09-05, 999🔥, 0💬

What Are Translation Tables
What Are Translation Tables? Translation tables, also called codon tables, are conversion tables that map 3-nucleobase combinations into amino acids to form protein sequences. It is known that all organisms do not use exactly the same translation table. But they vary from a standard translation tabl... 2023-03-17, 994🔥, 0💬

editor.options() - Get Editor Options
How to get a list of options used by the Ketcher editor with the editor.options() method? If you want to get a list of options used by the Ketcher editor, you can use the editor.options() method on the Ketcher Editor interface. Here is an HTML document that shows you how to get a list of options cur... 2023-11-18, 993🔥, 0💬

Retrieve Record Summary with Bio.Entrez.esummary()
How to Retrieve Record Summary with Bio.Entrez.esummary() function? Bio.Entrez.esummary() function allows you to retrieve summary information of a given record in a given NCBI Databas. It uses the Entrez Web services provided by www.ncbi.nlm.nih.gov. 1. Retrieve summary information from the "nlmcata... 2023-08-09, 993🔥, 0💬

addSphere() - Create Spheres
How to create spheres with 3Dmol.js addSphere() methods? viewer.addSphere() method in the $3Dmol.GLViewer class allows you to create sphere objects. Here is the signature of the addSphere() method: {$3Dmol.GLViewer} addSphere({SphereStyleSpec} spec) -&gt; {$3Dmol.GLShape} Here is an HTML code ex... 2023-09-07, 990🔥, 0💬

Pre-defined Sequence Alignment Score Settings
How to Use Pre-defined Sequence Alignment Score Settings? Biopython provides 3 Pre-defined Sequence Alignment Score Settings: "blastn" and "megablast" for nucleotide alignments, and "blastp" for protein alignments. Here is an example on how to "blastp" score settings. fyicenter$ python &gt;&... 2023-08-03, 989🔥, 0💬

UI Components of Online 3Dmol Viewer
What functions are supported by UI components on the Online 3Dmol Viewer? UI components on the Online 3Dmol Viewer support the following functions: 1. Model Data Input: Accessible through the "File/PDB/URL" menu item. You can load PDB protein data from the online PDB database, molecule compound data... 2023-09-07, 985🔥, 0💬

Create Motif With Biopython Bio.motifs Module
How to Create Motif With Biopython Bio.motifs Module? Biopython Bio.motifs Module allows you to create a motif object with a list of DNA or protein sequences. A motif object actually represents a sample set of sequences that matches a sequence motif pattern. 1. Create a motif object with a single se... 2023-07-11, 985🔥, 0💬

Install Online 3Dmol Viewer on Linux
How to install Online 3Dmol Viewer on my local Linux computer? The easiest way to use the Online 3Dmol Viewer is through the hosted server at https://3dmol.org/viewer.html . But if you want to have full control of the Online 3Dmol Viewer and faster response time, you can host it yourself on a Linux ... 2023-09-10, 984🔥, 0💬

Use BioJava with "Maven" Build Tool
How to Use BioJava with "Maven" Build Tool? If you want to install one or more BioJava Libraries with Maven, you can include BioJava libraries as dependencies in the Maven project file as shown in this tutorial. 1. Make sure that you have JDK installed. fyicenter$ javac -version javac 17.0.1 2. Make... 2023-04-25, 972🔥, 0💬

Single Sequence Record in FASTA Format
How to read a Single Sequence Record in FASTA Format? If you want to store additional information to a DNA or protein sequence, you can use the Bio.SeqRecord class, which contains the following properties: seq – The sequence itself as a Seq object. id – The primary ID used to identify the sequence. ... 2023-04-04, 971🔥, 0💬

What Is Ketcher File Format
What is Ketcher File Format? A Ketcher file is a JSON document that stores the entire content created in the Ketcher editor. It supports the following features: Supports molecule 3-D structures. Supports chemical reactions. Supports styled text labels. Supports S-Groups. Here is a simple example of ... 2024-02-11, 968🔥, 0💬

Load Data from Another HTML Element
How to load molecule data from another HTML element into the Embedded 3Dmol Viewer? You can use "data-element" and "data-type" attributes on the DIV element to load molecule data another HTML element into the Embedded 3Dmol Viewer. Here is an HTML code example, Embedded-Viewer-data-element.h tml,tha... 2023-01-31, 968🔥, 0💬

What Is Biopython
What is BioJava? Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. Biopython versions and release dates are: Biopython 1.80, November 18, 2022 Main features of Biopython: The ability to parse bioinformatics files into Py... 2023-02-04, 965🔥, 0💬

What Is OBF (Open Bioinformatics Foundation)
What Is OBF (Open Bioinformatics Foundation)? OBF (Open Bioinformatics Foundation) is a non-profit, volunteer-run group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. Currently, OBF supports the follow... 2023-02-04, 965🔥, 0💬

Motif PSSM with Bio.motifs
How to Calculate Motif PSSM with Bio.motifs Module? PSSM (Position-Specific Scoring Matrix), also referred as PSWM (Position-Specific Weight Matrix) or LSM (Logodds Scoring Matrix), represents how well the frequency of each letter at each position matches with a given background frequency. PSSM can ... 2023-07-01, 964🔥, 0💬

Ketcher File Structure for Molecule
What is the Ketcher file structure for a molecule structure? To represent a single molecule in a Ketcher file, you need to include a referenced-object in the "nodes" array as shown below: { "root": { "nodes": [ { "$ref": "mol&lt;seq&gt;" } ] }, "mol&lt;seq&gt;": { "type": "molecule",... 2024-03-07, 955🔥, 0💬

Motif Counts and Consensus with Bio.motifs
How to Get Motif Counts and Consensus with Bio.motifs Module? Motif counts represent how often each letter appears at each position in a motif sample set. Motif counts is also called PFM (Position Frequency Matrix). Motif consensus is the sequence of letters along the positions of the motif for whic... 2023-07-05, 955🔥, 0💬

editor.struct().loops - Get Loop List
How to get a list of loops currently in the Ketcher editor with the editor.struct().loops property? If you want to get a list of loops currently in the Ketcher editor, you can use the editor.struct().loops property on the Ketcher Editor interface. Here is an HTML document that shows you how to get a... 2023-11-23, 953🔥, 0💬

Calculate Substitutions in Alignments
How to Calculate Substitutions in Sequence Alignments? The substitutions property of an alignment reports how often letters in the alignment are substituted for each other. This is calculated by taking all pairs of rows in the alignment, counting the number of times two letters are aligned to each o... 2023-08-03, 944🔥, 0💬

Too Many Results from align() Function
Why there are So Many Results from the align() Function? If you are using the default score settings, you may get a very large number of possible alignments. Here is an example using the first and the third sequences from the PF05371_seed.faa file. fyicenter$ python &gt;&gt;&gt; from Bio... 2023-05-09, 944🔥, 0💬

Failed to Load D4DF9EC9DD21B943E35F3D5696D5D2A1.cache.js
Why JSME editor is not showing after upgrade to the 2022-09-26 version? If you upgraded JSME to the 2022-09-26 version from an older version, the JSME editor may fail to show up in your browser. In the browser developer console, you will see that a required JSME JavaScript file, D4DF9EC9DD21B943E35F... 2023-04-13, 941🔥, 0💬

Biopython - Tools for Biological Computation
Where to find FAQ (Frequently Asked Questions) on Biopython - Tools for Biological Computation? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on Biopython - Tools for Biological Computation. What Is Biopython Install Biopython Play with the Bio.... 2023-02-04, 940🔥, 0💬

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Atom Biology General Molecule Reaction Tools Trial Virus