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Lista de recursos estudada na disciplina de Bioinformática

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Lista de recursos estudada na disciplina de Bioinformática
- Base de dados:
NCBI (National Center for Biotechnology Information): https://www.ncbi.nlm.nih.gov/
Uniprot (Universal Protein Resource): https://www.uniprot.org/
Para acessar o Swiss-Prot, clique sobre o ícone deste banco de dados ou então acesse diretamente por
<https://www.uniprot.org/uniprot/?query=reviewed:yes>
KEGG (Kyoto Encyclopedia of Genes and Genomes): https://www.genome.jp/kegg/
Para acessar o Kegg Enzyme, clique sobre o ícone, que está na sessão “data-oriented entry points, ou
então acesse diretamente por <https://www.genome.jp/kegg/annotation/enzyme.html>
GO (Gene Ontology Consortium): http://www.geneontology.org/
- Alinhamento
BLAST (Basic Local Alignment Search Tool): https://blast.ncbi.nlm.nih.gov/Blast.cgi
Clustal Omega: https://www.ebi.ac.uk/Tools/msa/clustalo/
MEGA – instalado no seu computador
- Mapa de restrição de DNA
Rebase (Restriction Enzymne Database): http://tools.neb.com/REBsites/index.php
NebCutter (New England BioLabs): http://tools.neb.com/NEBcutter2/
WebCutter: http://heimanlab.com/cut2.html
TACG Restriction Mapping: http://biotools.umassmed.edu/tacg4/
- Parâmetros de sequências de nucleotídeos
Genomatix: http://www.genomatix.de/cgi-bin/tools/tools.pl
Repeat Masker: http://www.repeatmasker.org/cgi-bin/WEBRepeatMasker
Gramene: http://www.gramene.org/db/markers/ssrtool
- Desenho de primer
Primer3 Plus: http://primer3plus.com/cgi-bin/dev/primer3plus.cgi
Oligo Analyzer: https://www.idtdna.com/calc/analyzer
Oligo Calc: http://www.basic.northwestern.edu/biotools/oligocalc.html
- Parâmetros de sequências de aminoácidos
TagIdent (ExPASy): http://ca.expasy.org/tools/tagident.html
ProtParam (ExPASy): http://ca.expasy.org/tools/protparam.html
ProtScale (ExPASy): https://web.expasy.org/protscale/
Physico-chemical Profiles (PRABI): https://npsa-prabi.ibcp.fr/cgibin/npsa_automat.pl?page=npsa_pcprof.html
JaMBW (Java-based Molecular Biologist’s Workbench): http://www.bioinformatics.org/JaMBW/3/1/7/
DisProt: http://www.disprot.org/
RONN: https://www.strubi.ox.ac.uk/RONN
DisEMBL: http://dis.embl.de/
- Mapa de restrição de proteína
Peptide Cutter: http://ca.expasy.org/tools/peptidecutter/
- Predição de estruturas, sítios ativos e domínios
Sosui: http://harrier.nagahama-i-bio.ac.jp/sosui/sosui_submit.html
Split: http://split.pmfst.hr/split/4/
Octopus: http://octopus.cbr.su.se/
Phobius: http://phobius.sbc.su.se/
Rhythm: http://proteinformatics.charite.de/rhythm/index.php?site=helix
TMMOD: http://liao.cis.udel.edu/website/servers/TMMOD/scripts/frame.php?p=submit
TMHMM: http://www.cbs.dtu.dk/services/TMHMM/
Coiled-Coil Prediction (PRABI): https://npsa-prabi.ibcp.fr/cgibin/npsa_automat.pl?page=npsa_lupas.html
Coils (ExPASy): https://embnet.vital-it.ch/software/COILS_form.html
PairCoil2: http://cb.csail.mit.edu/cb/paircoil2/paircoil2.html
MarCoil: https://bcf.isb-sib.ch/webmarcoil/webmarcoilC1.html
2-ZIP Server: http://2zip.molgen.mpg.de/index.html
Helix-Turn-Helix Motif Prediction (PRABI): https://npsa-prabi.ibcp.fr/cgibin/npsa_automat.pl?page=npsa_hth.html
Quick2D: https://toolkit.tuebingen.mpg.de/#/tools/quick2d
ProScan (PRABI): https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_proscan.html
SoftBerry: http://www.softberry.com/berry.phtml?topic=protcomp&group=help&subgroup=proloc
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