Lista de Ferramentas de Bioinformática
(Diferença entre revisões)
(→Aplicativos online e standalone) |
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[[Categoria:Bioinformática]] | [[Categoria:Bioinformática]] | ||
| − | + | =Aplicativos e ferramentas= | |
| − | =Online= | + | ==Online== |
| − | =Standalone= | + | ==Standalone== |
*[http://www.expasy.org/ Expert Protein Analysis System] | *[http://www.expasy.org/ Expert Protein Analysis System] | ||
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:Bioinformatics Software | :Bioinformatics Software | ||
| − | + | =Platforms= | |
*[http://www.python.org/ Python] | *[http://www.python.org/ Python] | ||
**[http://numpy.scipy.org/ Numpy] | **[http://numpy.scipy.org/ Numpy] | ||
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*[http://www.java.com/en/ Java] | *[http://www.java.com/en/ Java] | ||
| − | + | =Cluster Tools= | |
*[http://ganglia.sourceforge.net/ Ganglia] | *[http://ganglia.sourceforge.net/ Ganglia] | ||
*[http://gridengine.sunsource.net/ SGE] | *[http://gridengine.sunsource.net/ SGE] | ||
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*[[Tutorials:_Using_modules_to_load_applications|Modules]] | *[[Tutorials:_Using_modules_to_load_applications|Modules]] | ||
| − | + | =Análises de sequências e alinhamento= | |
| − | + | *[http://www.ebi.ac.uk/Tools/similarityandanalysis.html Embl Tools] | |
| − | + | :Bioinformatics Tools for Sequence Similarity &* Analysis Searching | |
| − | :Bioinformatics Tools for Sequence Similarity & | + | *[http://www.fundp.ac.be/sciences/biologie/urbm/bioinfo/esypred/ NCBI Tools] |
| − | + | *[http://www.fundp.ac.be/sciences/biologie/urbm/bioinfo/esypred/ EsyPred3D] | |
| − | + | ||
:Predição de estruturas protéicas 3D | :Predição de estruturas protéicas 3D | ||
| − | + | *[http://www.bioperl.org/wiki/Main_Page Bioperl] | |
:BioPerl is a toolkit of perl modules useful in building bioinformatics solutions in Perl. | :BioPerl is a toolkit of perl modules useful in building bioinformatics solutions in Perl. | ||
| − | + | *[http://blast.ncbi.nlm.nih.gov/Blast.cgi Blast NCBI Online] | |
:NCBI Basic Local Alignment Search Tool | :NCBI Basic Local Alignment Search Tool | ||
| − | + | *[http://www.codoncode.com/ CodonCode Aligner] | |
:CodonCode Aligner is an easy-to-use program for sequence assembly, contig editing, and mutation detection. | :CodonCode Aligner is an easy-to-use program for sequence assembly, contig editing, and mutation detection. | ||
| − | + | *[http://www.clustal.org/ Clustal] | |
:Multiple alignment of nucleic acid and protein sequences | :Multiple alignment of nucleic acid and protein sequences | ||
==Análises metagenômicas== | ==Análises metagenômicas== | ||
| − | + | *[http://ab.inf.uni-tuebingen.de/software/megan/ MEGAN] | |
:MEtaGenome ANalyzer | :MEtaGenome ANalyzer | ||
| − | + | *[http://ab.inf.uni-tuebingen.de/software/megan/ JCVI Metarep] | |
:Análises metagenômicas (necessita de sequencias anotadas) | :Análises metagenômicas (necessita de sequencias anotadas) | ||
| − | + | *[http://manatee.sourceforge.net/ JCVI Manatee] | |
:Software de anotação de sequências | :Software de anotação de sequências | ||
| − | + | *[http://www.jcvi.org/cms/research/projects/annotation-service/ JCVI Annotation service] | |
:Serviço de anotação de sequências | :Serviço de anotação de sequências | ||
| − | + | *[http://www.jcoast.net/ JCoast] | |
: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. | :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. | ||
| − | + | *[http://www.cebitec.uni-bielefeld.de/groups/brf/software/gendb_info/index.html GenDB] | |
:GenDB is a genome annotation system for prokaryotic genomes. | :GenDB is a genome annotation system for prokaryotic genomes. | ||
| − | + | *[http://metagenomics.anl.gov/ MG-RAST] | |
:The Metagenomics RAST (online) | :The Metagenomics RAST (online) | ||
| − | + | *[http://www.megx.net/portal/content/content.html MegX] | |
:Portal for marine ecological genomics | :Portal for marine ecological genomics | ||
| − | + | *[http://www.jgi.doe.gov/programs/GEBA/index.html JGI GEBA] | |
:The GEBA project is aimed at systematically filling in the gaps in sequencing along the bacterial and archaeal branches of the tree of life. | :The GEBA project is aimed at systematically filling in the gaps in sequencing along the bacterial and archaeal branches of the tree of life. | ||
| − | + | *[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi IMG GEBA] | |
:Integrated Microbial Genomes | :Integrated Microbial Genomes | ||
| − | + | *[http://nbc.ece.drexel.edu/index.php NBC] | |
:Naïve Bayesian Classification tool | :Naïve Bayesian Classification tool | ||
| − | + | *[http://webcarma.cebitec.uni-bielefeld.de/cgi-bin/webcarma.cgi WebCarma] ([http://webcarma.cebitec.uni-bielefeld.de/cgi-bin/webcarma.cgi?PAGE=uploadData&NEW=1&SESSIONKEY=c0a3ccf4700e2e40e7bd47f7ee30b1194ab674296657c2481066384c630eefac&EMAIL=leonardonormando@gmail.com login]) | |
:WebCARMA is a web-based system for the functional and taxonomic analysis of metagenomic DNA sequences. | :WebCARMA is a web-based system for the functional and taxonomic analysis of metagenomic DNA sequences. | ||
| − | + | *[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001061 PhyolOTU] | |
:A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data | :A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data | ||
| − | + | *[https://portal.camera.calit2.net/gridsphere/gridsphere?cid=home CAMERA 2.0] | |
:Community Cyberinfrastructure for Advanced Microbial Ecology Research & Analysis | :Community Cyberinfrastructure for Advanced Microbial Ecology Research & Analysis | ||
| − | + | *[https://img.jgi.doe.gov/cgi-bin/mer/main.cgi IMG MER] | |
:IMG Metagenomics | :IMG Metagenomics | ||
| − | + | *[http://greengenes.lbl.gov/cgi-bin/nph-index.cgi GreenGenes] | |
:The greengenes web application provides access to the current and comprehensive 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading. | :The greengenes web application provides access to the current and comprehensive 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading. | ||
| − | + | *[http://metaphyler.cbcb.umd.edu/ MetaPhyller] | |
:Estimating Bacterial Composition from Metagenomic Sequences (linux) | :Estimating Bacterial Composition from Metagenomic Sequences (linux) | ||
| − | + | *[http://weizhong-lab.ucsd.edu/metagenomic-analysis/ WebMGA] | |
:Ótimo framework com várias ferramentas online, como ORF_finder e fragGeneScan | :Ótimo framework com várias ferramentas online, como ORF_finder e fragGeneScan | ||
| − | + | *[http://omics.informatics.indiana.edu/FragGeneScan/ FragGeneScan] | |
:Orf finder tool | :Orf finder tool | ||
| − | + | *[http://bioinformatics.oxfordjournals.org/content/26/6/715.full STAMP] | |
:Statistical Analysis of Metagenomic Profile | :Statistical Analysis of Metagenomic Profile | ||
| − | + | *[http://www.encyclon.net/multiblast/MultiBlastX.htm MultiBlastX] | |
:compares a nucleotide query sequence translated in all reading frames against a protein sequence database | :compares a nucleotide query sequence translated in all reading frames against a protein sequence database | ||
| − | + | *[http://metagenomics.atc.tcs.com/SPHINX/ SPHINX] | |
:An algorithm for taxonomic binning of metagenomic sequences [http://bioinformatics.oxfordjournals.org/content/early/2010/10/28/bioinformatics.btq608.full.pdf Artigo] | :An algorithm for taxonomic binning of metagenomic sequences [http://bioinformatics.oxfordjournals.org/content/early/2010/10/28/bioinformatics.btq608.full.pdf Artigo] | ||
| − | + | *[http://metagenomics.atc.tcs.com/binning/DiScRIBinATE/ DiScRIBinATE] | |
:DiScRIBinATE is a similarity based binning method. | :DiScRIBinATE is a similarity based binning method. | ||
| − | + | *[http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6033151&tag=1 Parallel-META] | |
:A high-performance computational pipeline for metagenomic data analysis | :A high-performance computational pipeline for metagenomic data analysis | ||
==Blogs e Tutoriais== | ==Blogs e Tutoriais== | ||
| − | + | *[http://www.ncbi.nlm.nih.gov/feed/rss.cgi NCBI News] | |
:NCBI RSS feed | :NCBI RSS feed | ||
| − | + | *[http://hot-bioinformatics.blogspot.com/ What’s hot in Bioinformatics] | |
| − | + | ||
:A personal blog about interesting news on the field of Bioinformatics, computational biology and related stuff | :A personal blog about interesting news on the field of Bioinformatics, computational biology and related stuff | ||
| − | + | *[http://bioinformatictools.blogspot.com/ Bionformatics Tools] | |
| − | + | *[http://biostar.stackexchange.com/questions/112/your-favorite-bioinformatics-blogs Lista de blogs] | |
:Blogs de bioinformática | :Blogs de bioinformática | ||
| − | + | *[http://bcbio.wordpress.com/ Blue Collar bioinformatics] | |
| − | + | *[http://blog.mckuhn.de/ BioCS] | |
:biology as computational science | :biology as computational science | ||
| − | + | *[http://finchtalk.geospiza.com/ Finch Talk] | |
:Follow the conversation to learn how you can make the most of your data | :Follow the conversation to learn how you can make the most of your data | ||
| − | + | *[http://news.open-bio.org/news/ OBF] | |
:Open source bioinfomatics | :Open source bioinfomatics | ||
[http://www.mailund.dk/ Mailund] | [http://www.mailund.dk/ Mailund] | ||
:Computer science, bioinformatics, genetics, and everything in between | :Computer science, bioinformatics, genetics, and everything in between | ||
| − | + | *[http://learnr.wordpress.com/ Learning R] | |
:As the title says, tips to learn R | :As the title says, tips to learn R | ||
| − | + | *[http://www.helixsoft.nl/blog/ Helix Soft] | |
:Do mesmos desenvolvedores do [http://www.wikipathways.org/ wikiPathways] | :Do mesmos desenvolvedores do [http://www.wikipathways.org/ wikiPathways] | ||
| − | + | *[http://nsaunders.wordpress.com/ N Saunders] | |
| − | + | *[http://www.scivee.tv/ SciVee] | |
:Science Youtube | :Science Youtube | ||
| − | + | *[http://www.bioinformaticszen.com/ Bioinformatics Zen] | |
| − | + | *Aprendendo R | |
:[http://www.ats.ucla.edu/stat/r/ Learn R] | :[http://www.ats.ucla.edu/stat/r/ Learn R] | ||
:[http://leg.ufpr.br/Rpira/Rpira/ Curso R] | :[http://leg.ufpr.br/Rpira/Rpira/ Curso R] | ||
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:[http://cran.r-project.org/doc/contrib/Krijnen-IntroBioInfStatistics.pdf Applied statistics for bioinformatics using R] | :[http://cran.r-project.org/doc/contrib/Krijnen-IntroBioInfStatistics.pdf Applied statistics for bioinformatics using R] | ||
:[http://sourceforge.net/projects/tinn-r/ TINN-R] | :[http://sourceforge.net/projects/tinn-r/ TINN-R] | ||
| − | + | *[http://www.sciviews.org/SciViews-R/ SciViews] | |
:GUI for R | :GUI for R | ||
| − | + | *[http://www.bioconductor.org/ Bioconductor] | |
:Diversos pacotes de análise Bioinformatica | :Diversos pacotes de análise Bioinformatica | ||
| − | + | *[http://phylogenomics.blogspot.com/ Phylogenomics] | |
Blog of Jonathan A. Eisen, evolutionary biologist, microbiologist and genomics researcher, | Blog of Jonathan A. Eisen, evolutionary biologist, microbiologist and genomics researcher, | ||
| − | + | *[http://thirdreviewer.com/ Third Reviewer] | |
| − | + | *[http://clovr.org/category/blog/ CloVR] | |
:Automated Sequence Analysis from Your Desktop | :Automated Sequence Analysis from Your Desktop | ||
| − | + | =Análises estatísticas= | |
| − | + | *[http://www.r-project.org/ R] | |
| − | + | ||
:The R Project for Statistical Computing | :The R Project for Statistical Computing | ||
| − | + | *[http://rstudio.org/ RStudio] | |
:RStudio™ is a new integrated development environment (IDE) for R. | :RStudio™ is a new integrated development environment (IDE) for R. | ||
Edição de 11h27min de 26 de abril de 2012
Tabela de conteúdo |
Aplicativos e ferramentas
Online
Standalone
- 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
- Wiki com uma lista de banco de dados biológicos
- QB3 Python Bioinformatics Course 2010
- GMOD is the Generic Model Organism Database project, a collection of open source software tools for creating and managing genome-scale biological databases
- Ferramentas on-line de alinhamento e criação de árvores
- Interative Tree of Life
- Compara réplicas de T-RFLP
- The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis.
- A prokaryotic 16S rRNA Gene sequence database with phylotypes that represent uncultured species
- Metagenomic ORF finder
- Gene Prediction in Metagenomes and Novel Prokaryotes by Heuristic Approach
- Artemis is a free genome browser and annotation tool that allows visualisation of sequence features
- 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.
- Teste de modelos de alinhamento
- 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.
- LNCC Sabia Metagenomic tool
- Bioinformatics Lab (Labinfo) of the National Laboratory of Scientific Computation of the Ministry of Science and Technology (MCT) of Brazil
- Database for Annotation, Visualization and Integrated Discovery (DAVID )
- Scripts em BioPerl
- BL!P: BLAST in Pivot
- Cyrille2 - Cyrille2 Wiki
- SEAStAR | Armbrust Lab
- Lectures - Intro | Programming For Biologists
- Glimmer-MG :: Center for Bioinformatics and Computational Biology
- Bioinformatics Scripts NERC Institute
- Learn Python the hard way
- Angus 2.0
- Biological Database List | Nucleic Acid Research
Idaho University - IBEST Applications (home brew!)
- MiCA Microbial Community Analysis
- HiTSA High Throughput Sequence Analysis
- Statgen Genetic Distances Statistical Generator
Sequence Analysis
Sequence Alignment
Phylogenetic Congruence
Phylogenetic Inference
- FastDNAml
- Garli
- GeneTree
- Mesquite
- ModelTest
- MrBayes
- P4
- PAML
- PAUP
- Seq-Gen
- Phylip
- Phyml
- RAxML
- RAxML web
- TreeView
- BEAST
Population Genetics
Protein Structure
Statistical/Mathematical Packages
Contig Assembly
Misc
- Metastats: Detect Differentially Abundant Features
- Lista de Ferramentas
- Bioinformatics Software
Platforms
Cluster Tools
Análises de sequências e alinhamento
- Bioinformatics Tools for Sequence Similarity &* Analysis Searching
- Predição de estruturas protéicas 3D
- BioPerl is a toolkit of perl modules useful in building bioinformatics solutions in Perl.
- NCBI Basic Local Alignment Search Tool
- CodonCode Aligner is an easy-to-use program for sequence assembly, contig editing, and mutation detection.
- Multiple alignment of nucleic acid and protein sequences
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
- Computer science, bioinformatics, genetics, and everything in between
- As the title says, tips to learn R
- Do mesmos desenvolvedores do wikiPathways
- Science Youtube
- Bioinformatics Zen
- Aprendendo R
- 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.
