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

MTKVYANSIQQHLCLD SLT GPVRSVLTQGTTAEKERVVDRIALLERCLDP SNSLPPVRSVLTQGTTAEKVQLVVSCLGVVCSIICLALGIAAAAVTAKRL VAVAVATILAVALLVVAGLLFSGVLCSPVSVLAASLFFGVGAFLLGGALV GGVLTTEAVTRERLHRSQTLMWNNLCCKTAEVEQKISTASANAKSNDKTR KLGE

Seq 200

MECVKQLCRNHLCLD SLT GPVRSVLTQGTTAEKVQLVVSCLGVVCSIICL 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!

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