OBF (Open Bioinformatics Foundation) Tools

Q

Where to find molecule FAQ (Frequently Asked Questions)? I want to learn more about OBF (Open Bioinformatics Foundation) and its software tools.

✍: FYIcenter.com

A

Here is a large collection of tutorials to answer many frequently asked questions compiled by FYIcenter.com team about OBF (Open Bioinformatics Foundation) and its software tools:

About OBF (Open Bioinformatics Foundation)

What Is OBF (Open Bioinformatics Foundation)

Biopython - Tools for Biological Computation

What Is Biopython

Install Biopython

Play with the Bio.Seq Module

Double Stranded DNA, mRNA and Transcription

mRNA, Protein and Translation

What Are Translation Tables

Single Sequence Record in FASTA Format

Single Sequence Record in GenBank Format

Play with the ls_orchid.fasta File

List NCBI Databases with Bio.Entrez.einfo()

Search NCBI Databases with Bio.Entrez.esearch()

Retrieve Record Summary with Bio.Entrez.esummary()

Fetch Sequences from NCBI with Bio.Entrez.efetch()

Search for Related Items in NCBI with Bio.Entrez.elink()

Global Query on All NCBI Databases with Bio.Entrez.egquery()

Search History with Bio.Entrez for Subsequent Calls

Fetch Sequences from SwissProt with Bio.ExPASy.get_sprot_raw()

Scan Prosite Database with Bio.ExPASy.ScanProsite.scan()

Read Sequence Alignments with Bio.AlignIO

Calculate Substitutions in Alignments

Fetch Sequences from NCBI with Bio.Blast.NCBIWWW.qblast()

Use Bio.SearchIO Module to Parse BLAST XML Result

Parse PDB Entry with Bio.PDB.MMCIFParser.parser Module

Calculate Pairwise Sequence Alignment

Pairwise Sequence Alignment Score Settings

Too Many Results from align() Function

Pre-defined Sequence Alignment Score Settings

Get Help Documentation with Biopython

Biopython for Sequence Motif Analysis

What Is Sequence Motif Analysis

Create Motif With Biopython Bio.motifs Module

Motif Counts and Consensus with Bio.motifs

Read Motif in JASPAR Format with Bio.motifs

Motif PCM, PFM, PPM, PWM with Bio.motifs

Motif PSSM with Bio.motifs

Sequence Score against PSSM with Bio.motifs

Search for Motif Matches with Bio.motifs

Compare Motifs Using PSSM with Bio.motifs

Motif ICM with Bio.motifs

Motif ICM as Relative Divergence with Bio.motifs

Motif ICM Logo with WebLogo Tools

BioJava - Java Bioinformatics Toolkit

What Is BioJava

BioJava Library Installation Options

Use BioJava with "Maven" Build Tool

Read FASTA File with FastaReaderTeat.java

"mvn dependency:build-classpath" - Generate Class Pass

BioPerl - Perl Bioinformatics Toolkit

What Is BioPerl

BioPerl Modules Installation Options

HOWTO Documents at BioPerl.org

Install BioPerl Package with "cpanm"

Install BioPerl Package Manually

⇒ About OBF (Open Bioinformatics Foundation)

2023-02-04, 1872🔥, 0💬

Molecule FYI-1002129
Molecule Summary: ID: FYI-1002129 Names: InChIKey: IZFHEQBZOYJLPK-UHFFFAOYSA-N SMILES: O=C(O)CCCCC(S)CCS Received at FYIcenter.com on: 2023-02-03 2023-03-17, 1409🔥, 0💬

Molecule FYI-1002130
Molecule Summary: ID: FYI-1002130 Names: InChIKey: MJJWBJFYYRAYKU-UHFFFAOYSA-N SMILES: CC6=CC7c3c(O)cc(c2cc1ccc(O)cc1 o2)cc3OC8(c4ccc(O)cc4O)Oc5cc(O )ccc5C(C6)C78Received at FYIcenter.com on: 2023-02-03 2023-03-17, 1401🔥, 0💬

Molecule FYI-1002128
Molecule Summary: ID: FYI-1002128 Names: InChIKey: CULUWZNBISUWAS-UHFFFAOYSA-N SMILES: O=C(Cn1ccnc1N(=O)=O)NCc2ccccc2 Received at FYIcenter.com on: 2023-02-02 2023-04-04, 1328🔥, 0💬

Molecule FYI-1002132
Molecule Summary: ID: FYI-1002132 Names: InChIKey: XCUYWJKMSJIDKM-UHFFFAOYSA-N SMILES: CC(=O)CO.CC(=O)CO Received at FYIcenter.com on: 2023-02-04 2023-03-17, 1326🔥, 0💬

Molecule FYI-1002131
Molecule Summary: ID: FYI-1002131 Names: InChIKey: FCEOBCBWDCMLAV-YECYYMRXSA-N SMILES: C=C(C)[C@@]26O[C@@]8(c1ccccc1) O[C@@H]2[C@@H]5[C@@H]3O[C@]3(C O)[C@@H](O)[C@]4(O)C(=O)C(C)=C [C@H]4[C@]5(C[C@H]6OC(=O)/C=C/ C=C/c7ccccc7)O8Received at FYIcenter.com on: 2023-02-03 2023-03-17, 1255🔥, 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, 636🔥, 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, 555🔥, 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, 554🔥, 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, 521🔥, 0💬

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