MCIC Bioinformatics Resources

The MCIC provides services for

Capillary sequencing using the ABI 3100xl
Genotyping: fragment analysis on Beckman CEQ8800, SNP analysis on Luminex200 or Illumina BeadXpress
Deep genome sequencing using the Illumina Genome Analyzer II.

Bioinformatics

Services

Computational support to scientists involved in genomics research includes
- development of automation scripts for personalized data base searches
- training and help with the use of the software on the Linux workstation maintained at the facility
- training and help with Perl, Bio-Perl and C++
For bioinformatics projects or questions contact Saranga Wijeratne.

MCIC software

Links to some bioinformatics site of general interest

Bioinformatics tools:

NCBI BLAST home page: http://www.ncbi.nlm.nih.gov/BLAST/
Institute for genomic research: http://www.tigr.org/bioinformatics.shtml
How to dual boot your desktop to run Linux and Windows: http://www.geocities.com/epark/linux/grub-w2k-HOWTO.html
Bioinformatics software: http://www.netsci.org/Resources/Software/Bioinform/databases.html
Article: E. A. Greene & S. Henikoff, Getting more from your sequence on the web: http://www.nature.com/ng/web_specials/gazing/
Links to many useful molecular resources tools and databases, including bioinformatics sites: This is where you might go to browse and find if there are any new programs or databases that might be helpful for you. http://bioinformatics.ca/links_directory/
Nucleic Acids Research review of websites and databases: This is updated annually and provides a short summary of what is available at various databases and webservers. WAMBA organizers will look for a person each year to provide a short overview of what is available.
2009 review of databases: http://nar.oxfordjournals.org/content/vol37/suppl_1/index.dtl
2008 review of webservers: http://nar.oxfordjournals.org/content/vol36/suppl_2/index.dtl
List of genomes being sequenced and their status: This is about as complete as we can find and provides useful links, status reports and contact information for various genome projects. http://www.ncbi.nlm.nih.gov/genomes/leuks.cgi
Phylogenetics pipeline website: This is a useful website that allows one to go from a list of concatenated FASTA files to a phylogenetic tree, all in one, easy to use format. http://www.phylogeny.fr/
File conversion (web based): This website allows one to convert from one file type to another easily. http://www-bimas.cit.nih.gov/molbio/readseq/
File conversion (download): Conversion software. http://iubio.bio.indiana.edu/soft/molbio/readseq/java/
Sequence Maniputation Suite: software available for use on your desktops that allows for some basic manipulations of sequence information. http://www.bioinformatics.org/sms2/mirror.html
SNP database (focus on crop plants): This is a site to watch as it currently only has information for barley, brassica, and rice but may add additional crops later. http://autosnpdb.qfab.org.au/
SNP database: This is a SNP annotation, selection and prioritization system. It can also be used for analysis and interpretation of SNP data. http://www.snplogic.org/
SNP visualization software: http://genome.lbl.gov/vista/snpvista/

Societies and discussion groups:

International Society for Computational Biology: http://www.iscb.org
To participate in the ISCB discussion: http://www.sdsc.edu/pb/iscb/iscb-edu.html
The Bioperl Project is an international association of developers of open source Perl tools for bioinformatics, genomics and life science research: http://bio.perl.org
The Open Bioinformatics Foundation is an umbrella group for the various bio*.org projects that grew out of the original BioPerl project: http://www.open-bio.org
Bioinformatics.Org is an international organization which provides free and open resources for research, development and education so that such resources can be further developed. The organization is nonprofit and maintains an Internet site by the same name where these resources can be accessed: http://bioinformatics.org

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