RAYCHAUDHURI LAB @ CSIR-CCMB, Hyderabad
Gene ontology
The Ontologizer: A Tool for Statistical Analysis and Visualization of High-Throughput Biological Data Using Gene Ontology -
http://compbio.charite.de/contao/index.php/ontologizer2.html
DAVID Bioinformatics Resources 6.7 -
http://david.abcc.ncifcrf.gov/
,
http://www.nature.com/nprot/journal/v4/n1/pdf/nprot.2008.211.pdf
REVIGO -
http://revigo.irb.hr/
Sequence analysis
ExPASy (proteomics) -
http://www.expasy.org/proteomics
ExPASy (genomics) -
http://www.expasy.org/genomics
Tango -
http://tango.crg.es/
FoldIndex -
http://bip.weizmann.ac.il/fldbin/findex
UCL Bioinformatics group -
http://bioinf.cs.ucl.ac.uk/
Protein-protein interaction
BIANA: Biologic Interaction and Network Analysis -
http://sbi.imim.es/web/index.php/research/servers/biana?
The Human Protein Reference Database (HPRD) -
http://www.hprd.org/
BioGRID | Database of Protein and Genetic Interactions -
http://thebiogrid.org/
ProPrInt: Protein - Protein Interaction Predictor -
http://www.imtech.res.in/raghava/proprint/resources.html
IntAct -
http://www.ebi.ac.uk/intact/
Interaction network analysis
Cytoscape -
http://www.cytoscape.org/
STRING - Known and Predicted Protein-Protein Interactions -
http://string-db.org/
Pathway analysis
KEGG: Kyoto Encyclopedia of Genes and Genomes -
http://www.genome.jp/kegg/
PANTHER -
http://www.pantherdb.org/
,
http://www.nature.com/nprot/journal/v8/n8/pdf/nprot.2013.092.pdf
MS data analysis
Mascot Server -
http://www.matrixscience.com/search_form_select.html
MaxQuant -
http://www.maxquant.org/
Perseus -
http://www.perseus-framework.org/
Statistics
SciStatCalc -
http://scistatcalc.blogspot.co.uk/2013/11/home.html
GraphPad -
http://www.graphpad.com/quickcalcs/
Molecular and cell biology tools
https://www.neb.com/tools-and-resources/usage-guidelines/cloning-guide
https://www.neb.com/tools-and-resources/usage-guidelines/cleavage-close-to-the-end-of-dna-fragments
http://tools.neb.com/NEBcutter2/
https://www.neb.com/tools-and-resources/interactive-tools/double-digest-finder?
http://www.thermoscientificbio.com/webtools/reviewer/
http://www.genomics.agilent.com/primerDesignProgram.jsp
Useful databases
NCBI -
http://www.ncbi.nlm.nih.gov/
Ensembl -
http://asia.ensembl.org/index.html
GeneCards -
http://www.genecards.org/
The Human Protein Atlas -
http://www.proteinatlas.org/
ProteomicsDB -
https://www.proteomicsdb.org/
Miscellaneous
GENE-E -
http://www.broadinstitute.org/cancer/software/GENE-E/index.html
gitools -
http://www.gitools.org/
BioMath Calculators -
http://www.promega.in/resources/tools/biomath-calculators/
BioVenn -
http://www.cmbi.ru.nl/cdd/biovenn/
addgene -
http://www.addgene.org/
Whitehead BaRC public tools -
http://jura.wi.mit.edu/bioc/tools/
COLORBREWER 2.0 -
http://colorbrewer2.org/
HD Community BioRepository -
http://www.ccr.coriell.org/Sections/Collections/CHDI/?SsId=45
Copyright (C) 2014, Swasti Raychaudhuri. All rights reserved.
