Cool BaRC Web Tools

Prat Thiru

BaRC Web Toolshttp://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_126167NM_126168 NM_322122XM_322082 NR_210999XM_322084 NR_001321NM_126168

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_001321NM_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.htmlhttp://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 AnalysisMap Genes to Pathways

http://iona.wi.mit.edu/yuan/gene2pathway/

•Determine which pathway genes might be involved from different databases.

Functional AnalysisIdentify 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

Functional AnalysisWalk up GO ontologies to get more general "induced" terms

http://iona.wi.mit.edu/bell/go/

•Find more general GO terms

Functional AnalysisTabulate the number of codons in sequence data

http://iona.wi.mit.edu/gurdziel/CodonCounter/CodonCounter.html

•Determine codon usage in a sequence

VisualizationProtein Sequence Visualization Tool

http://iona.wi.mit.edu/cgi-bin/walker/draw_enrichment.pl

•Color codes amino acids

Visualization

Sequence Word Viewer

http://iona.wi.mit.edu/rodriguez/wordview/

•Display occurrences of a motif

Seq 55MTKVYANSIQQHLCLDSLTGPVRSVLTQGTTAEKERVVDRIALLERCLDPSNSLPPVRSVLTQGTTAEKVQLVVSCLGVVCSIICLALGIAAAAVTAKRLVAVAVATILAVALLVVAGLLFSGVLCSPVSVLAASLFFGVGAFLLGGALVGGVLTTEAVTRERLHRSQTLMWNNLCCKTAEVEQKISTASANAKSNDKTRKLGE

Seq 200MECVKQLCRNHLCLDSLTGPVRSVLTQGTTAEKVQLVVSCLGVVCSIICLALGIAAAAVGVSCSGFAIGLGVIAILLGIVLFAISALDVLEDHGLVGAASLFFGVGAFLLGGALVGGCPFKLPCKSSPANEPTVQFFKGKNGSADKVILVTQ

TargetScan

http://www.targetscan.org/

•Find predicted targets of miRNA

Need a tool?

Let us know!

wibr-bioinformatics@wi.mit.edu