Lista de Ferramentas de Bioinformática

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[[Categoria:Bioinformática]]
 
[[Categoria:Bioinformática]]
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=ORGANIZAR EM UMA DAS CATEGORIAS ABAIXO=
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=Aplicativos e ferramentas=
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*[http://www.ebi.ac.uk/Tools/similarityandanalysis.html Embl Tools]
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:Bioinformatics Tools for Sequence Similarity &amp* Analysis Searching
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*[http://www.fundp.ac.be/sciences/biologie/urbm/bioinfo/esypred/ NCBI Tools]
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*[http://www.fundp.ac.be/sciences/biologie/urbm/bioinfo/esypred/ EsyPred3D]
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:Predição de estruturas protéicas 3D
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*[http://www.bioperl.org/wiki/Main_Page Bioperl]
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:BioPerl is a toolkit of perl modules useful in building bioinformatics solutions in Perl.
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*[http://blast.ncbi.nlm.nih.gov/Blast.cgi Blast NCBI Online]
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:NCBI Basic Local Alignment Search Tool
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*[http://www.codoncode.com/ CodonCode Aligner]
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:CodonCode Aligner is an easy-to-use program for sequence assembly, contig editing, and mutation detection.
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*[http://www.clustal.org/ Clustal]
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:Multiple alignment of nucleic acid and protein sequences
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==Online==
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==Standalone==
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*[http://www.expasy.org/ Expert Protein Analysis System]
 
*[http://www.expasy.org/ Expert Protein Analysis System]
 
:ExPASy is the new SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools in different areas of life sciences
 
:ExPASy is the new SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools in different areas of life sciences
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*[http://img.jgi.doe.gov/ Integrated Microbial Genomes System]
 
*[http://img.jgi.doe.gov/ Integrated Microbial Genomes System]
 
:The Integrated Microbial Genomes (IMG) is a genome browsing and annotation system
 
:The Integrated Microbial Genomes (IMG) is a genome browsing and annotation system
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*[http://en.wikipedia.org/wiki/List_of_biological_databases List of biological databases]
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:Wiki com uma lista de banco de dados biológicos
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*[http://intro-prog-bioinfo-2010.wikispaces.com/ Python Bioinformatics Course]
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:QB3 Python Bioinformatics Course 2010
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*[http://gmod.org/wiki/Main_Page GMOD]
 
*[http://gmod.org/wiki/Main_Page GMOD]
 
:GMOD is the Generic Model Organism Database project, a collection of open source software tools for creating and managing genome-scale biological databases
 
:GMOD is the Generic Model Organism Database project, a collection of open source software tools for creating and managing genome-scale biological databases
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*[http://www.phylogeny.fr/version2_cgi/index.cgi Phylogeny.fr]
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:Ferramentas on-line de alinhamento e criação de árvores
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*[http://itol.embl.de/index.shtml iTol]
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:Interative Tree of Life
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*[http://inismor.ucd.ie/%7Etalign/index.html t-Align]
 
*[http://inismor.ucd.ie/%7Etalign/index.html t-Align]
 
:Compara réplicas de T-RFLP
 
:Compara réplicas de T-RFLP
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*[http://www.arb-home.de/ ARB]
 
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:The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis.
 
  
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*[http://www.sanger.ac.uk/resources/software/artemis/ Artemis]
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:Artemis is a free genome browser and annotation tool that allows visualisation of sequence features
  
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*[http://eztaxon-e.ezbiocloud.net/images/taxon/eztaxon-e_bi.png Ez-Taxon]
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*[http://www.ecoevol.ufg.br/sam/ Spatial Analisys in Macroecology]
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:A prokaryotic 16S rRNA Gene sequence database with phylotypes that represent uncultured species
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:SAM (Spatial Analysis in Macroecology) is a program designed as a package of tools for spatial statistical analysis, mainly for applications in Surface Pattern Spatial Analysis.
  
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*[http://david.abcc.ncifcrf.gov/ David]
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:Database for Annotation, Visualization and Integrated Discovery (DAVID )
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=Análise de sequências=
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==Aplicativos Online==
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==Aplicativos Standalone==
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*[http://www.codoncode.com/ CodonCode Aligner]
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:CodonCode Aligner is an easy-to-use program for sequence assembly, contig editing, and mutation detection.
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=Alinhamento de sequências=
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==Aplicativos Online==
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*[http://blast.ncbi.nlm.nih.gov/Blast.cgi Blast NCBI Online]
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:NCBI Basic Local Alignment Search Tool
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*[http://www.ebi.ac.uk/Tools/similarityandanalysis.html Embl Tools]
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:Bioinformatics Tools for Sequence Similarity & Analysis Searching
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*[http://www.fundp.ac.be/sciences/biologie/urbm/bioinfo/esypred/ EsyPred3D]
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:Predição de estruturas protéicas 3D
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*[http://www.phylogeny.fr/version2_cgi/index.cgi Phylogeny.fr]
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:Ferramentas on-line de alinhamento e criação de árvores
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*[http://itol.embl.de/index.shtml iTol]
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:Interative Tree of Life
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*[http://darwin.uvigo.es/software/jmodeltest.html ModelTest]
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:Teste de modelos de alinhamento
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==Aplicativos Standalone==
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*[http://www.clustal.org/ Clustal]
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:Multiple alignment of nucleic acid and protein sequences
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*[http://www.megasoftware.net/ MEGA]
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:MEGA is an integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, inferring ancestral sequences, and testing evolutionary hypotheses.
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==Bancos de Dados Biológicos==
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*[http://en.wikipedia.org/wiki/List_of_biological_databases List of biological databases]
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:Wiki com uma lista de banco de dados biológicos
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*[http://www.arb-home.de/ ARB]
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:The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis.
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=Classificação e taxonomia=
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==Aplicativos Online==
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*[http://eztaxon-e.ezbiocloud.net/images/taxon/eztaxon-e_bi.png Ez-Taxon]
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:A prokaryotic 16S rRNA Gene sequence database with phylotypes that represent uncultured species
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==Aplicativos Standalone==
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=Análises Metagenômica=
  
 
*[http://orphelia.gobics.de/ Orphelia]
 
*[http://orphelia.gobics.de/ Orphelia]
 
:Metagenomic ORF finder
 
:Metagenomic ORF finder
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*[http://exon.biology.gatech.edu/metagenome/Prediction/ MetaGene Mark]
 
*[http://exon.biology.gatech.edu/metagenome/Prediction/ MetaGene Mark]
 
:Gene Prediction in Metagenomes and Novel Prokaryotes by Heuristic Approach
 
:Gene Prediction in Metagenomes and Novel Prokaryotes by Heuristic Approach
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*[http://www.sanger.ac.uk/resources/software/artemis/ Artemis]
 
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:Artemis is a free genome browser and annotation tool that allows visualisation of sequence features
 
  
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*[http://www.megasoftware.net/ MEGA]
 
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:MEGA is an integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, inferring ancestral sequences, and testing evolutionary hypotheses.
 
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*[http://darwin.uvigo.es/software/jmodeltest.html ModelTest]
 
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:Teste de modelos de alinhamento
 
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*[http://www.ecoevol.ufg.br/sam/ Spatial Analisys in Macroecology]
 
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:SAM (Spatial Analysis in Macroecology) is a program designed as a package of tools for spatial statistical analysis, mainly for applications in Surface Pattern Spatial Analysis.
 
 
*[http://www.sabiametagenome.lncc.br/login Sabia Metagenome]
 
*[http://www.sabiametagenome.lncc.br/login Sabia Metagenome]
 
:LNCC Sabia Metagenomic tool
 
:LNCC Sabia Metagenomic tool
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*[http://www.labinfo.lncc.br/ LabInfo LNCC]
 
*[http://www.labinfo.lncc.br/ LabInfo LNCC]
 
:Bioinformatics Lab (Labinfo) of the National Laboratory of Scientific Computation of the Ministry of Science and Technology (MCT) of Brazil
 
:Bioinformatics Lab (Labinfo) of the National Laboratory of Scientific Computation of the Ministry of Science and Technology (MCT) of Brazil
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=Análises Estatísticas=
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=Plataformas de Desenvolvimento=
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*[http://www.bioperl.org/wiki/Main_Page Bioperl]
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:BioPerl is a toolkit of perl modules useful in building bioinformatics solutions in Perl.
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*[http://www.bioperl.org/wiki/Bioperl_scripts Bioperl Scripts]
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:Scripts em BioPerl
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=Blogs e Tutoriais=
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*[http://intro-prog-bioinfo-2010.wikispaces.com/ Python Bioinformatics Course]
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:QB3 Python Bioinformatics Course 2010
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=Aplicativos e ferramentas=
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 +
 +
  
  
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*[http://david.abcc.ncifcrf.gov/ David]
 
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:Database for Annotation, Visualization and Integrated Discovery (DAVID )
 
  
  
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*[http://www.bioperl.org/wiki/Bioperl_scripts Bioperl Scripts]
 
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:Scripts em BioPerl
 
  
  

Edição de 11h51min de 26 de abril de 2012

Tabela de conteúdo

ORGANIZAR EM UMA DAS CATEGORIAS ABAIXO

ExPASy is the new SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools in different areas of life sciences
The Integrated Microbial Genomes (IMG) is a genome browsing and annotation system
GMOD is the Generic Model Organism Database project, a collection of open source software tools for creating and managing genome-scale biological databases
Compara réplicas de T-RFLP
Artemis is a free genome browser and annotation tool that allows visualisation of sequence features
SAM (Spatial Analysis in Macroecology) is a program designed as a package of tools for spatial statistical analysis, mainly for applications in Surface Pattern Spatial Analysis.
Database for Annotation, Visualization and Integrated Discovery (DAVID )



Análise de sequências

==Aplicativos Online==

==Aplicativos Standalone== *CodonCode Aligner :CodonCode Aligner is an easy-to-use program for sequence assembly, contig editing, and mutation detection.


Alinhamento de sequências

==Aplicativos Online== *Blast NCBI Online :NCBI Basic Local Alignment Search Tool

*Embl Tools :Bioinformatics Tools for Sequence Similarity & Analysis Searching

*EsyPred3D :Predição de estruturas protéicas 3D

*Phylogeny.fr :Ferramentas on-line de alinhamento e criação de árvores

*iTol :Interative Tree of Life

*ModelTest :Teste de modelos de alinhamento

==Aplicativos Standalone== *Clustal :Multiple alignment of nucleic acid and protein sequences

*MEGA :MEGA is an integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, inferring ancestral sequences, and testing evolutionary hypotheses.

==Bancos de Dados Biológicos== *List of biological databases :Wiki com uma lista de banco de dados biológicos

*ARB :The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis.

Classificação e taxonomia

==Aplicativos Online== *Ez-Taxon :A prokaryotic 16S rRNA Gene sequence database with phylotypes that represent uncultured species

==Aplicativos Standalone==

Análises Metagenômica

Metagenomic ORF finder
Gene Prediction in Metagenomes and Novel Prokaryotes by Heuristic Approach
LNCC Sabia Metagenomic tool
Bioinformatics Lab (Labinfo) of the National Laboratory of Scientific Computation of the Ministry of Science and Technology (MCT) of Brazil

Análises Estatísticas

Plataformas de Desenvolvimento

*Bioperl :BioPerl is a toolkit of perl modules useful in building bioinformatics solutions in Perl.

*Bioperl Scripts :Scripts em BioPerl

Blogs e Tutoriais

*Python Bioinformatics Course :QB3 Python Bioinformatics Course 2010


Aplicativos e ferramentas



Idaho University - IBEST Applications (home brew!)

Sequence Analysis

Sequence Alignment

Phylogenetic Congruence

Phylogenetic Inference

Population Genetics

Protein Structure

Statistical/Mathematical Packages

Contig Assembly

Misc


Metastats: Detect Differentially Abundant Features
Lista de Ferramentas
Bioinformatics Software

Platforms

Cluster Tools

Análises metagenômicas

MEtaGenome ANalyzer
Análises metagenômicas (necessita de sequencias anotadas)
Software de anotação de sequências
Serviço de anotação de sequências
JCoast is a next-generation software solution for the exploration, mining and comparison of your genome and metagenome projects. Based on a set of predicted and automatically annotated ORFs (a genome or metagenome) it acts as a window into these preprocessed data which does not only allow to view the initial results but also facilitates improved annotation and in-depth data analysis.
GenDB is a genome annotation system for prokaryotic genomes.
The Metagenomics RAST (online)
Portal for marine ecological genomics
The GEBA project is aimed at systematically filling in the gaps in sequencing along the bacterial and archaeal branches of the tree of life.
Integrated Microbial Genomes
Naïve Bayesian Classification tool
WebCARMA is a web-based system for the functional and taxonomic analysis of metagenomic DNA sequences.
A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data
Community Cyberinfrastructure for Advanced Microbial Ecology Research & Analysis
IMG Metagenomics
The greengenes web application provides access to the current and comprehensive 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading.
Estimating Bacterial Composition from Metagenomic Sequences (linux)
Ótimo framework com várias ferramentas online, como ORF_finder e fragGeneScan
Orf finder tool
Statistical Analysis of Metagenomic Profile


compares a nucleotide query sequence translated in all reading frames against a protein sequence database


An algorithm for taxonomic binning of metagenomic sequences Artigo
DiScRIBinATE is a similarity based binning method.
A high-performance computational pipeline for metagenomic data analysis

Blogs e Tutoriais

NCBI RSS feed
A personal blog about interesting news on the field of Bioinformatics, computational biology and related stuff
Blogs de bioinformática
biology as computational science
Follow the conversation to learn how you can make the most of your data
Open source bioinfomatics

Mailund

Computer science, bioinformatics, genetics, and everything in between
As the title says, tips to learn R
Do mesmos desenvolvedores do wikiPathways
Science Youtube
Learn R
Curso R
Introdução à estatística básica com R
Applied statistics for bioinformatics using R
TINN-R
GUI for R
Diversos pacotes de análise Bioinformatica

Blog of Jonathan A. Eisen, evolutionary biologist, microbiologist and genomics researcher,

Automated Sequence Analysis from Your Desktop

Análises estatísticas

The R Project for Statistical Computing
RStudio™ is a new integrated development environment (IDE) for R.
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