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
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