Bioinformatic Is Cool, I Mean Really Cool

I’ve been fascinated by genomic research for years.  While successfully implementing a fairly large and diverse set of algorithms (segmentation, image processing and machine learning) on text, image and other semi-structured datasets, till recently I didn’t have much exposure to the exciting field of bioinformatics, processing DNA and RNA sequences.

After completing Bioinformatics Methods I  and Bioinformatics Methods II (thank you Professor Nicholas Provart, University of Toronto) I have a better appreciation of the important roles of Bioinformatics in medicinal sciences and in drug discovery, diagnosis and disease management, but also a better appreciation of the complexity involved with the processing of large biological datasets.

Topics covered in these two courses include multiple sequence alignments, phylogenetics, gene expression data analysis, and protein interaction networks, in two separate parts. The first part, Bioinformatic Methods I, dealt with databases, Blast, multiple sequence alignments, phylogenetics, selection analysis and metagenomics. The second part, Bioinformatic Methods II, dealt with motif searching, protein-protein interactions, structural bioinformatics, gene expression data analysis, and cis-element predictions.

Please find below a short list of tools and resources I’ve used while completing the different labs:

NCBI/Blast I

http://www.ncbi.nlm.nih.gov/

Multiple Sequence Alignments

http://megasoftware.net (download tool)

http://dialign.gobics.de/

http://mafft.cbrc.jp/alignment/server/

Phylogenetic

https://code.google.com/p/jmodeltest2/

http://www.megasoftware.net/

http://evolution.genetics.washington.edu/phylip.html

http://bar.utoronto.ca/webphylip/

http://mobyle.pasteur.fr/cgi-bin/portal.py#forms::fastdnaml

Selection Analysis

http://selecton.tau.ac.il/

http://bar.utoronto.ca/EMBOSS

http://www.datamonkey.org/                 

NEXT GENERATION SEQUENCING APPLICATIONS: RNA-SEQ AND METAGENOMICS                                    

http://mpss.udel.edu

http://mockler-jbrowse.mocklerlab.org/jbrowse.athal/?loc=Chr2%3A12414112..12415692

http://www.ncbi.nlm.nih.gov/pubmed/20410051

METAGENOMICS

http://metagenomics.anl.gov/

Protein Domain, Motif and Profile Analysis

http://www.ncbi.nlm.nih.gov/guide/domains-structures/

http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi               

http://smart.embl-heidelberg.de/

http://pfam.xfam.org/search

http://www.ebi.ac.uk/InterProScan/

Protein-protein interactions               

http://mips.gsf.de/proj/ppi/  

http://dip.doe-mbi.ucla.edu/dip/Main.cgi

http://www.thebiogrid.org/index.php

http://www.cytoscape.org/download.html   (download tool)             

Structural Bioinformatics

http://pdb.org  

http://www.ncbi.nlm.nih.gov/Structure/VAST/vastsearch.html  

http://pymol.org/edu (download tool)            

Gene Expression Analysis

http://www.ncbi.nlm.nih.gov/sra  

http://bar.utoronto.ca/BioC/

Gene Expression Data Analysis

http://bar.utoronto.ca/ntools/cgi-bin/ntools_expression_angler.cgi

http://bar.utoronto.ca/affydb/cgi-bin/affy_db_exprss_browser_in.cgi

http://bioinfo.cau.edu.cn/agriGO/analysis.php

http://bar.utoronto.ca/efp/

http://atted.jp/

http://bar.utoronto.ca/ntools/cgi-bin/ntools_venn_selector.cgi

Cis regulatory element mapping and prediction

http://bar.utoronto.ca/ntools/cgi-bin/BAR_Promomer.cgi

http://www.bioinformatics2.wsu.edu/cgi-bin/Athena/cgi/home.pl

http://jaspar.genereg.net/

http://meme-suite.org/tools/meme

Additional Coursers

https://class.coursera.org/molevol-002 Computational Molecular Evolution

https://www.coursera.org/course/pkubioinfo Bioinformatics

https://www.coursera.org/course/programming1 Python

https://www.coursera.org/course/webapplications Web Applications (Ruby on Rails)

https://www.coursera.org/course/epigenetics Epigenetics

https://www.coursera.org/course/genomicmedicine Genomic & Precision Medicine

https://www.coursera.org/course/usefulgenetics Useful Genetics

Book

Zvelebil & Baum 2008 Understanding Bioinformatics. Garland Science, New York