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Cool BaRC Web Tools

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

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Cool BaRC Web Tools

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  1. Cool BaRC Web Tools Prat Thiru

  2. 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

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

  4. General Analysis and File Utilities • Find what is common and unique between two listsNM_126167 NM_126167 • NM_126168 NM_322122 • XM_322082 NR_210999 • XM_322084 • NR_001321 • NM_126168 Compare Two Lists http://iona.wi.mit.edu/bell/compare.html

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

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

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

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

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

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

  11. EntrezGene/RefSeq/UniGene/SGD/GenBank annotation • Retrieve UTRs/CDS from GenBank flat file Extract UTRs and/or CDS regions from GenBank sequences 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 • Convert gene ids from Entrez to Ensembl Entrez Gene IDs  Ensembl IDs  http://iona.wi.mit.edu/bell/locuslink-db-7.html

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

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

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

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

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

  19. Visualization • Display occurrences of a motif Sequence Word Viewer Seq 55MTKVYANSIQQHLCLDSLTGPVRSVLTQGTTAEKERVVDRIALLERCLDPSNSLPPVRSVLTQGTTAEKVQLVVSCLGVVCSIICLALGIAAAAVTAKRLVAVAVATILAVALLVVAGLLFSGVLCSPVSVLAASLFFGVGAFLLGGALVGGVLTTEAVTRERLHRSQTLMWNNLCCKTAEVEQKISTASANAKSNDKTRKLGESeq 200MECVKQLCRNHLCLDSLTGPVRSVLTQGTTAEKVQLVVSCLGVVCSIICLALGIAAAAVGVSCSGFAIGLGVIAILLGIVLFAISALDVLEDHGLVGAASLFFGVGAFLLGGALVGGCPFKLPCKSSPANEPTVQFFKGKNGSADKVILVTQ http://iona.wi.mit.edu/rodriguez/wordview/

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

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

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