C. Victor Jongeneel, Ph.D.
Director of HPCBio
2002 Institute for Genomic Biology
1206 W. Gregory Drive, Urbana, IL 61801
Phone: (217) 244-6632
FAX: (217) 265-6800
Email: vjongene@illinois.edu
Roy J. CarverUniversity of Illinois
Biotechnology Center
Links
Databases
- EMBL http://www.ebi.ac.uk/embl/
- ENSEMBL http://www.ensembl.org/
- NCBI http://www.ncbi.nlm.nih.gov/
- TIGR http://www.tigr.org/
- SWISS-PROT http://www.expasy.org/sprot/ and http://www.ebi.ac.uk/swissprot/
Analysis tools
- NCBI tools - http://www.ncbi.nlm.nih.gov/Tools/index.html
- TIGR tools - http://www.tigr.org/software/
- EMBL-EBI - http://www.ebi.ac.uk/services/
- Softberry - http://www.softberry.com/berry.phtml (genomic.sanger.ac.uk)
- MIT tools - http://genes.mit.edu/
Some commonly used tools
- Trinity - http://trinityrnaseq.sourceforge.net/
- Velvet - http://genome.cshlp.org/content/18/5/821.long
- Cufflinks - http://cufflinks.cbcb.umd.edu/
- TopHat - http://tophat.cbcb.umd.edu/
- Bowtie - http://bowtie-bio.sourceforge.net/index.shtml
- Abyss - http://www.bcgsc.ca/platform/bioinfo/software/abyss
- Soap - http://soap.genomics.org.cn/soapdenovo.html
- BLAST - http://www.ncbi.nlm.nih.gov/BLAST/
- CLUSTALW - http://www.ebi.ac.uk/clustalw/
- Reverse Complement - http://www.ualberta.ca/~stothard/javascript/rev_comp.html
- Codon usage -
http://gcua.schoedl.de/ - Translation - http://www.bioinformatics.vg/bioinformatics_tools/JVT.shtml
- Genefinder - http://www.softberry.com/berry.phtml?topic=index&group=programs&subgroup=gfind
- GENSCAN - http://genes.mit.edu/GENSCAN.html
- ORF finder - http://www.ncbi.nlm.nih.gov/gorf/gorf.html