Atom Biology General Molecule Reaction Tools Trial Virus

1 2 3 > >>   ∑:57  Sort:Date

"mvn dependency:build-classpath" - Generate Class Pass
How to generate class path for dependences with Maven? If you run your application JAR file generated from Maven, you need to include JAR files of all dependences in the class path. One way to build this class path is to use the "mvn dependency:build-classpath" command. 1. Generate class path of all... 2023-04-17, 732🔥, 0💬

OBF (Open Bioinformatics Foundation) Tools
Where to find molecule FAQ (Frequently Asked Questions)? I want to learn more about OBF (Open Bioinformatics Foundation) and its software tools. Here is a large collection of tutorials to answer many frequently asked questions compiled by FYIcenter.com team about OBF (Open Bioinformatics Foundation)... 2023-02-04, 491🔥, 0💬

Pairwise Sequence Alignment Score Settings
How to change Pairwise Sequence Alignment Score Settings? Bio.Align.PairwiseAligner().al ign()uses a set of Alignment Score Settings to control how each possible alignment score is calculated. It then returns only those alignments that have the highest score. Here are the Alignment Score Settings th... 2023-05-09, 396🔥, 0💬

Play with the ls_orchid.fasta File
How to download and process ls_orchid.fasta file? ls_orchid.fasta file is an example of DNA sequence file in FASTA format provided in the Biopython source code package. You can also download it and use it to test Biopython library. 1. Download ls_orchid.fasta. fyicenter$ curl https://raw.githubuserc... 2023-07-08, 382🔥, 0💬

Calculate Pairwise Sequence Alignment
How to Calculate Pairwise Sequence Alignment? You can use the Bio.Align.PairwiseAligner() function to Calculate Pairwise Sequence Alignment. It uses the Needleman-Wunsch, Smith-Waterman, Gotoh (three-state), and Waterman-Smith-Beyer global and local pairwise alignment algorithms. Here is an example ... 2023-05-09, 376🔥, 0💬

Install BioPerl Package Manually
How to install BioPerl package manually? I am having trouble using the "cpan/cpanm" command. If you are having problems using the "cpan/cpanm" command, you can following this tutorial to install the BioPerl 1.7.7 distribution package manually. 1. Go to metacpan.org/pod/BioPerl . 2. Click "Download (... 2024-02-05, 365🔥, 2💬

Scan Prosite Database with Bio.ExPASy.ScanProsite.scan()
How to Scan Prosite Database with Bio.ExPASy.ScanProsite.scan() function? Bio.ExPASy.ScanProsite.scan() function allows to scan the Prosite database with a given sequence. Here is an example on how to Scan Prosite Database. fyicenter$ python >>> from Bio.ExPASy import ScanProsit... 2023-09-05, 361🔥, 0💬

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> 1fat.... 2023-05-09, 360🔥, 0💬

Install BioPerl Package with "cpanm"
How to install BioPerl package with "cpanm" command? Using "cpanm" command is the best option to install the BioPerl distribution package automatically as shown in this tutorial on a CentOS computer: 1. Make sure that you have "cpanm" command installed. If not run the command below: fyicenter$ sudo ... 2023-02-28, 358🔥, 0💬

Biopython for Sequence Motif Analysis
Where to find FAQ (Frequently Asked Questions) on Biopython for Sequence Motif Analysis? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on Biopython for Sequence Motif Analysis. What Is Sequence Motif Analysis Create Motif With Biopython Bio.moti... 2023-07-29, 349🔥, 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 >>> from Bio... 2023-05-09, 348🔥, 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, 340🔥, 0💬

Motif PCM, PFM, PPM, PWM with Bio.motifs
How to Calculate Motif PCM, PFM, PPM, and PWM with Bio.motifs Module? There are several statistical matrices associated with a sequence motif sample set. PCM (Position Count Matrix) - PCM contains Counts of occurrences of each letter at each position. We can get PCM with "counts" property of a motif... 2023-07-01, 339🔥, 0💬

Install Biopython
How to install Biopython? The easiest way to install Biopython is to use the "pip" command as shown below. 1. Make sure that Python 3 is installed. fyicenter$ python --version Python 3.8.8 2. Install Biopython. fyicenter$ pip install biopython Requirement already satisfied: numpy in ... Installing c... 2023-02-04, 339🔥, 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, 336🔥, 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, 334🔥, 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, 333🔥, 0💬

BioPerl Modules Installation Options
What are installation options for BioPerl modules? There are several ways to install one or more BioPerl modules. 1. Using "cpanm" command - Run "cpanm ..." to install the given module automatically from cpan.org repository, if have "cpanm" installed. For example, run "cpanm Bio::SeqIO" to install B... 2023-03-07, 327🔥, 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, 325🔥, 0💬

What Is BioPerl
What is BioPerl? BioPerl is a toolkit of perl modules useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the bioperl-live repository consist of the core of the functio... 2023-04-05, 323🔥, 0💬

BioJava Library Installation Options
What are installation options for BioJava Library? There are several ways to install BioJava Library. 1. Using "Maven" build tool - Add BioJava as a dependency to your project pom.xml file: <dependencies> <dependency> <groupId>org.bio java</groupId&... 2023-04-25, 322🔥, 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, 321🔥, 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, 321🔥, 0💬

Fetch Sequences from SwissProt with Bio.ExPASy.get_sprot_raw()
How to Fetch Sequences from SwissProt with Bio.ExPASy.get_sprot_raw() function? SwissProt with Bio.ExPASy.get_sprot_raw() function allows you to fetch protein sequences from SwissProt database. Here is an example on how to Fetch Sequences from SwissProt. fyicenter$ python >>> fr... 2023-09-10, 320🔥, 0💬

1 2 3 > >>   ∑:57  Sort:Date

Atom Biology General Molecule Reaction Tools Trial Virus