Transcript Slides
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/
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