1. Cool BaRC Web Tools Prat Thiru

2. BaRC Web Tools http://iona.wi.mit.edu/bio/tools/bioc_tools.html http://iona.wi.mit.edu/bio/tools/bioc_tools.html We have tools for: General Analysis and File Utilities Genomics EntrezGene/RefSeq/UniGene/SGD/GenBank annotation Homology (Orthology) Converting IDs between databases Functional Analysis Visualization

3. General Analysis and File Utilities Venn Diagram Generator Show the number of items shared and unique between two sets http://jura.wi.mit.edu/bioc/tools/venn.html

4. General Analysis and File Utilities Compare Two Lists Find what is common and unique between two lists NM_126167 NM_126167 NM_126168 NM_322122 XM_322082 NR_210999 XM_322084 NR_001321 NM_126168 http://iona.wi.mit.edu/bell/compare.html

5. General Analysis and File Utilities Redundant List Analysis Count the number of occurrences in a list NM_126167 NM_126168 XM_322082 XM_322084 NR_001321 NM_126168 http://iona/cedrone/redundant/

6. General Analysis and File Utilities Submatrix Selector Select specific rows and columns in a file http://iona.wi.mit.edu/bell/submatrix_selector/

7. Genomics Genomic Sequence Extractor Retrieve sequence up/down stream for a list of genomic location(s) http://iona.wi.mit.edu/bell/extract_custom.html

8. Genomics RefSeq Regulatory Extractor Retrieve regions around transcription start or end site http://iona.wi.mit.edu/bell/refseq_extractor.html

9. Genomics Merge Overlapping Genome Regions Collapse overlapping regions into a single region http://iona.wi.mit.edu/bell/merge_regions/merge_regions.html

10. EntrezGene/RefSeq/UniGene/SGD/GenBank annotation Entrez Gene IDs  info Get information for a list of Entrez Gene IDs http://iona.wi.mit.edu/walker/webtools/locuslink-db-0.html

11. EntrezGene/RefSeq/UniGene/SGD/GenBank annotation Extract UTRs and/or CDS regions from GenBank sequences Retrieve UTRs/CDS from GenBank flat file http://iona.wi.mit.edu/bell/utrs/

12. Homology (Orthology) Find orthologous Ensembl IDs http://iona.wi.mit.edu/bell/homology/ensembl.html http://iona.wi.mit.edu/bell/comparative/

13. Converting IDs between Databases Entrez Gene IDs  Ensembl IDs Convert gene ids from Entrez to Ensembl http://iona.wi.mit.edu/bell/locuslink-db-7.html 

14. Functional Analysis Map Genes to Pathways http://iona.wi.mit.edu/yuan/gene2pathway/ Determine which pathway genes might be involved from different databases.

15. Functional Analysis Identify over-represented GO terms in a gene set http://iona.wi.mit.edu/yuan/go_anno/ Find out which GO categories are over-represented in the GO terms

16. Functional Analysis Walk up GO ontologies to get more general "induced" terms http://iona.wi.mit.edu/bell/go/ Find more general GO terms

17. Functional Analysis Tabulate the number of codons in sequence data http://iona.wi.mit.edu/gurdziel/CodonCounter/CodonCounter.html Determine codon usage in a sequence

18. Visualization Protein Sequence Visualization Tool http://iona.wi.mit.edu/cgi-bin/walker/draw_enrichment.pl Color codes amino acids

19. Visualization Sequence Word Viewer http://iona.wi.mit.edu/rodriguez/wordview/ Display occurrences of a motif Seq 55 MTKVYANSIQQHLCLDSLTGPVRSVLTQGTTAEKERVVDRIALLERCLDP SNSLPPVRSVLTQGTTAEKVQLVVSCLGVVCSIICLALGIAAAAVTAKRL VAVAVATILAVALLVVAGLLFSGVLCSPVSVLAASLFFGVGAFLLGGALV GGVLTTEAVTRERLHRSQTLMWNNLCCKTAEVEQKISTASANAKSNDKTR KLGE Seq 200 MECVKQLCRNHLCLDSLTGPVRSVLTQGTTAEKVQLVVSCLGVVCSIICL ALGIAAAAVGVSCSGFAIGLGVIAILLGIVLFAISALDVLEDHGLVGAAS LFFGVGAFLLGGALVGGCPFKLPCKSSPANEPTVQFFKGKNGSADKVILV TQ

20. TargetScan http://www.targetscan.org/ Find predicted targets of miRNA

21. Need a tool? Let us know! wibr-bioinformatics@wi.mit.edu