Atom Biology General Molecule Reaction Tools Trial Virus

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Parse PDB Entry with Bio.PDB.MMCIFParser.parser Module
How to Parse PDB Entry with Bio.PDB.MMCIFParser.parser.get _structure()function? Bio.PDB.MMCIFParser.parser.get _structure()function allows you to parse and any PDB (Protein Database) data files. 1. Download a PDB file in PDB format. fyicenter$ curl http://files.rcsb.org/view/1fa t.pdb&gt; 1fat.... 2023-05-09, 844🔥, 0💬

What Is BioJava
What is BioJava? BioJava is a open-source Java library for bioinformatics. BioJava versions and release dates are: BioJava 6.1.0 BioJava 6.0.0 BioJava 5.3.0 BioJava 5.2.0 BioJava 5.0.0 BioJava 4.2.9 BioJava 4.2.1 BioJava 4.2.0 BioJava legacy 1.9.1 Main modules of BioJava: The Core Module (biojava-co... 2023-04-26, 842🔥, 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, 840🔥, 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, 839🔥, 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, 837🔥, 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, 830🔥, 0💬

Fetch Sequences from NCBI with Bio.Blast.NCBIWWW.qblast()
How to Fetch Sequences from NCBI with Bio.Blast.NCBIWWW.qblast()? The function qblast() in the Bio.Blast.NCBIWWW module allows you to call the online version of BLAST to fetch DNA or protein sequences from https://blast.ncbi.nlm.nih.gov /Blast.cgi.Currently the qblast() function only works with 5 BL... 2023-05-09, 826🔥, 0💬

List NCBI Databases with Bio.Entrez.einfo()
How to List NCBI Databases with Bio.Entrez.einfo() function? Bio.Entrez.einfo() function allows you to list NCBI Databases and their related information. It uses the Entrez Web services provided by www.ncbi.nlm.nih.gov. 1. Get a list of NCBI databases. fyicenter$ python &gt;&gt;&gt; from... 2023-07-08, 824🔥, 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, 815🔥, 0💬

Use Bio.SearchIO Module to Parse BLAST XML Result
How to Use Bio.SearchIO Module to Parse BLAST XML Result? The Bio.SearchIO module allows to parse sequence search result from different result format. 1. Try the following code to query the "nt" database under the "blastn" program with a given DNA sequence, which is reverse translated from a protein... 2023-05-09, 812🔥, 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, 812🔥, 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, 811🔥, 0💬

HOWTO Documents at BioPerl.org
What tutorials are provided at BioPerl.org? BioPerl.org provides the following tutorials in the format of HOWTO documents: Beginners HOWTO - Introduction to BioPerl for biologists. Features and Annotations HOWTO - Reading and writing detailed data associated with sequences. BlastPlus HOWTO - Create,... 2023-03-07, 803🔥, 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, 801🔥, 0💬

Single Sequence Record in GenBank Format
How to read a Single Sequence Record in GenBank Format? The GenBank format for DNA or protein sequences contains more properties and a better structure that FASTA format. You can follow these steps to download GenBank file example and create a Bio.SeqRecord object. 1. Download an example of a Sequen... 2023-04-04, 800🔥, 0💬

Search for Motif Matches with Bio.motifs
How to Search for Matches in a Target Sequence again a motif with Bio.motifs? Bio.motifs module offers two options to search for segments that match a motif in a target sequence. 1. Use the motif instances to search for exact matches. fyicenter$ python &gt;&gt;&gt; from Bio.Seq import Se... 2023-06-19, 793🔥, 0💬

Get Help Documentation with Biopython
How to Get Help Documentation with Biopython? Biopython has help documentations built in the library. You can use the help() to read them. Read help documentation on Biopython library. fyicenter$ python &gt;&gt;&gt; import Bio &gt;&gt;&gt; help(Bio) Help on package Bio: NAME ... 2023-07-29, 787🔥, 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, 773🔥, 0💬

Motif ICM Logo with WebLogo Tools
How to Create Motif ICM Logo with WebLogo Tools? Motif ICM Logo is a graphical representation of the ICM (Information Content Matrix). Motif ICM Logo is also referred as Multiple Sequence Alignment Logo, Sequence Conservation Logo, or Sequence Logo. You can use the WebLogo tool provided by US Berkel... 2023-04-26, 763🔥, 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, 762🔥, 0💬

About OBF (Open Bioinformatics Foundation)
Where to find FAQ (Frequently Asked Questions) in understanding what is OBF (Open Bioinformatics Foundation)? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team in understanding what is OBF (Open Bioinformatics Foundation). What Is OBF (Open Bioinfor... 2023-02-04, 759🔥, 0💬

Play with the Bio.Seq Module
How to import the Bio.Seq module and use its functions? Here are some examples on how to import the Bio.Seq module and use its functions. 1. Import the Bio.Seq module and create a Bio.Seq object. fyicenter$ python &gt;&gt;&gt; from Bio.Seq import Seq &gt;&gt;&gt; my_seq = Seq... 2023-02-04, 755🔥, 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, 751🔥, 0💬

BioJava - Java Bioinformatics Toolkit
Where to find FAQ (Frequently Asked Questions) on BioJava - Java toolkit for computational molecular biology? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on BioJava - Java toolkit for computational molecular biology. What Is BioJava BioJava Li... 2023-04-26, 749🔥, 0💬

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Atom Biology General Molecule Reaction Tools Trial Virus