Atom Biology General Molecule Reaction Tools Trial Virus

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Sequence Score against PSSM with Bio.motifs
How to Calculate Sequence Score against PSSM with Bio.motifs? With the motif PSSM (Position-Specific Scoring Matrix) defined in the previous tutorial, we can define a matching score of any given sequence against the motif: score = sum_over_j(PSSM[S[j], j]) where: S[i] is a given sequence PSSM[i, j] ... 2023-06-19, 312🔥, 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, 311🔥, 0💬

Compare Motifs Using PSSM with Bio.motifs
How to Compare Motifs Using PSSM with Bio.motifs? If you know PSSMs of two motifs, you can compare them using the PSSM's dist_pearson() function. It returns a position offset for the best alignment and a distance between the two motifs. 1. Create a shorter motif from a given PCM without actual insta... 2023-06-19, 310🔥, 0💬

Read FASTA File with FastaReaderTeat.java
How to read a FASTA fie with FastaReaderTeat.java? If you compiled the example program, FastaReaderTeat.java, with Maven as shown in the previous tutorial, you can follow these steps to read a FASTA file. 1. Prepare a FASTA file, example.fasta. fyicenter$ cd bio fyicenter$ vi example.fasta &gt;s... 2023-04-17, 310🔥, 0💬

Motif ICM with Bio.motifs
How to Calculate Motif ICM with Bio.motifs Module? ICM (Information Content Matrices) represents how important of each position over others. ICM can be expressed as: ICM[i,j] = PPM[i,j]*(IC t - U[j]) where: PPM[i,j] is the Position Probability Matrix IC t is the total IC: log 2 (n) n is the number o... 2023-05-31, 309🔥, 0💬

What Is Online Server of 3Dmol Viewer
What Is Online Server of 3Dmol Viewer? Online Server of 3Dmol Viewer is an online service provided by University of Pittsburgh. It allows you to view 3-D structures of molecules including proteins interactively using the 3Dmol.js library. Main features of Online Server of 3Dmol Viewer are: support f... 2023-09-07, 308🔥, 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, 307🔥, 0💬

"style={...}:..." - Specify Style Attributes
How to Specify Style Attributes using the "style={...}:...,..." URL parameter in the Online 3Dmol Viewer? Style Attributes can be specified as a comma separated list of "key~value" tokens. For example, the following URL provided 3 style attributes for the "carton" style: https://3dmol.org/viewer.htm.. . 2023-09-07, 305🔥, 0💬

Fetch Sequences from NCBI with Bio.Entrez.efetch()
How to Fetch Sequences from NCBI with the Bio.Entrez.efetch() function? Bio.Entrez.efetch() function allows you to fetch DNA or protein sequences from NCBI databases: PubMed, GenBank, GEO, and many others. It uses the Entrez Web services provided by www.ncbi.nlm.nih.gov. Here is an example on how to... 2023-08-25, 304🔥, 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, 304🔥, 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, 304🔥, 0💬

$3Dmol.download('cid:...', ...) - Download CID Molecule
How to download molecule by CID with the $3Dmol.download() method? The syntax to download molecule by CID with the $3Dmol.download() method is shown below: $3Dmol.download("cid:{CID}", viewer, options, callback) -&gt; {$3Dmol.GLModel} viewer - The $3Dmol.GLViewer instance where the downloaded pr... 2023-01-11, 304🔥, 0💬

Code Bug in server.py in 3Dmol Source Code
Why am I getting the "Connection refused" error when accessing my local 3Dmol Viewer? If you are getting the "Connection refused" error when accessing your hosted 3Dmol Viewer over the network, it's most likely caused by the code bug in the server's Python source code. 1. Make sure that your 3Dmol V... 2023-02-19, 303🔥, 0💬

Search for Related Items in NCBI with Bio.Entrez.elink()
How to Search for Related Items in NCBI with Bio.Entrez.elink() function? Bio.Entrez.elink() function allows you to find related items in a NCBI database for a given record. It uses the Entrez Web services provided by www.ncbi.nlm.nih.gov. Here is an example on how to find related items with the Bio... 2023-08-25, 302🔥, 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, 302🔥, 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, 300🔥, 0💬

Global Query on All NCBI Databases with Bio.Entrez.egquery()
How to Global Query on All NCBI Databases with Bio.Entrez.egquery() function? Bio.Entrez.egquery() function allows you to perform a global search on all NCBI Databases for a given key word. It uses the Entrez Web services provided by www.ncbi.nlm.nih.gov. Here is an example on how to do a global sea... 2023-08-25, 298🔥, 0💬

Motif ICM as Relative Divergence with Bio.motifs
How to Calculate Motif ICM as Relative Divergence with Bio.motifs module? ICMRD (Information Content Matrices as Relative Divergence) represents how different a given PPM is from the uniform distribution. ICMRD can be expressed as: ICMRD[i,j] = PPM[i,j]*PSSM[i,j] where: PPM[i,j] is the Position Prob... 2023-05-31, 298🔥, 0💬

"new window.ResizeObserver(this.resize)" Error
Why am I getting the "error creating viewer: TypeError: undefined is not a constructor" error at "new window.ResizeObserver(this.res ize)"?If you load a 3Dmol.js HTML file in an older Apple Safari Web browser, you will get the following error in the browser developer console. error creating viewer: ... 2023-09-07, 297🔥, 0💬

What Is Sequence Motif Analysis
What is Sequence Motif Analysis? In biology, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and usually assumed to be related to biological function of the macromolecule. For example, an N-glycosylation site motif can be defined as Asn, followed by anything but Pr... 2023-07-11, 296🔥, 0💬

BioPerl - Perl Bioinformatics Toolkit
Where to find FAQ (Frequently Asked Questions) on BioPerl - Perl toolkit for computational molecular biology? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on BioPerl - Perl toolkit for computational molecular biology. What Is BioPerl BioPerl Mo... 2023-04-17, 296🔥, 0💬

Missing 3Dmol-min.js on Local 3Dmol Server
Why is my local 3Dmol server redirecting to browser to https://get.webgl.org/? If you access your local 3Dmol server with a browser, and you see the https://get.webgl.org/ Website displayed, it's most likely missing the 3Dmol-min.js file on the server. This may happen if 3Dmol server was not install... 2023-02-19, 296🔥, 0💬

addModel() - Add Model from Data
How to create a model from a molecule data string with 3Dmol.js addModel() methods? viewer.addModel() method in the $3Dmol.GLViewer class allows you to create a model from molecule data string: {$3Dmol.GLViewer} addModel(data, format, options) -&gt; {$3Dmol.GLModel} Here is an HTML code example,... 2023-01-11, 295🔥, 0💬

Search History with Bio.Entrez for Subsequent Calls
How to Use Search History with Bio.Entrez for Subsequent Calls? If use Bio.Entrez.esearch() and found a large number of matches, you can use the history feature to retrieve matched records in multiple sequence Bio.Entrez.efetch() calls. 1. Turn on the history feature in the esearch() call with the u... 2023-09-10, 294🔥, 0💬

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Atom Biology General Molecule Reaction Tools Trial Virus