Cool BaRC Web Tools
Prat Thiru
BaRC Web Tools
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
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
General Analysis and File Utilities
Compare Two Lists
•Find what is common and unique between two lists
NM_126167
NM_126168
XM_322082
XM_322084
NR_001321
NM_126168
NM_126167
NM_322122
NR_210999
http://iona.wi.mit.edu/bell/compare.html
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/
General Analysis and File Utilities
Submatrix Selector
•Select specific rows and columns in a file
http://iona.wi.mit.edu/bell/submatrix_selector/
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
Genomics
RefSeq Regulatory Extractor
•Retrieve regions around transcription start or end site
http://iona.wi.mit.edu/bell/refseq_extractor.html
Genomics
Merge Overlapping Genome Regions
•Collapse overlapping regions into a single region
http://iona.wi.mit.edu/bell/merge_regions/merge_regions.html
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
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/
Homology (Orthology)
•Find orthologous Ensembl IDs
http://iona.wi.mit.edu/bell/homology/ensembl.html
http://iona.wi.mit.edu/bell/comparative/
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
Functional Analysis
Map Genes to Pathways
•Determine which pathway genes might be involved from
different databases.
http://iona.wi.mit.edu/yuan/gene2pathway/
Functional Analysis
Identify over-represented GO terms in a gene set
•Find out which GO categories are over-represented in the
GO terms
http://iona.wi.mit.edu/yuan/go_anno/
Functional Analysis
Walk up GO ontologies to get more general "induced" terms
•Find more general GO terms
http://iona.wi.mit.edu/bell/go/
Functional Analysis
Tabulate the number of codons in sequence data
•Determine codon usage in a sequence
http://iona.wi.mit.edu/gurdziel/CodonCounter/CodonCounter.html
Visualization
Protein Sequence Visualization Tool
•Color codes amino acids
http://iona.wi.mit.edu/cgi-bin/walker/draw_enrichment.pl
Visualization
Sequence Word Viewer
•Display occurrences of a motif
Seq 55
MTKVYANSIQQHLCLDSLTGPVRSVLTQGTTAEKERVVDRIALLERCLDP
SNSLPPVRSVLTQGTTAEKVQLVVSCLGVVCSIICLALGIAAAAVTAKRL
VAVAVATILAVALLVVAGLLFSGVLCSPVSVLAASLFFGVGAFLLGGALV
GGVLTTEAVTRERLHRSQTLMWNNLCCKTAEVEQKISTASANAKSNDKTR
KLGE
Seq 200
MECVKQLCRNHLCLDSLTGPVRSVLTQGTTAEKVQLVVSCLGVVCSIICL
ALGIAAAAVGVSCSGFAIGLGVIAILLGIVLFAISALDVLEDHGLVGAAS
LFFGVGAFLLGGALVGGCPFKLPCKSSPANEPTVQFFKGKNGSADKVILV
TQ
http://iona.wi.mit.edu/rodriguez/wordview/
TargetScan
•Find predicted targets of miRNA
http://www.targetscan.org/
Need a tool?
Let us know!
wibr-bioinformatics@wi.mit.edu