Cool BaRC Web Tools Prat Thiru

BaRC Web Tools 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

General Analysis and File Utilities Compare Two Lists Find what is common and unique between two lists NM_ NM_ NM_ NM_ XM_ NR_ XM_ NR_ NM_

General Analysis and File Utilities Redundant List Analysis Count the number of occurrences in a list NM_ NM_ XM_ XM_ NR_ NM_

General Analysis and File Utilities Submatrix Selector Select specific rows and columns in a file

Genomics Genomic Sequence Extractor Retrieve sequence up/down stream for a list of genomic location(s)

Genomics RefSeq Regulatory Extractor Retrieve regions around transcription start or end site

Genomics Merge Overlapping Genome Regions Collapse overlapping regions into a single region

EntrezGene/RefSeq/UniGene/SGD/GenBank annotation Entrez Gene IDs  info Get information for a list of Entrez Gene IDs

EntrezGene/RefSeq/UniGene/SGD/GenBank annotation Extract UTRs and/or CDS regions from GenBank sequences Retrieve UTRs/CDS from GenBank flat file

Homology (Orthology) Find orthologous Ensembl IDs

Converting IDs between Databases Entrez Gene IDs  Ensembl IDs Convert gene ids from Entrez to Ensembl 

Functional Analysis Map Genes to Pathways Determine which pathway genes might be involved from different databases.

Functional Analysis Identify over-represented GO terms in a gene set Find out which GO categories are over-represented in the GO terms

Functional Analysis Walk up GO ontologies to get more general "induced" terms Find more general GO terms

Functional Analysis Tabulate the number of codons in sequence data Determine codon usage in a sequence

Visualization Protein Sequence Visualization Tool Color codes amino acids

Visualization Sequence Word Viewer Display occurrences of a motif Seq 55 MTKVYANSIQQHLCLDSLTGPVRSVLTQGTTAEKERVVDRIALLERCLDP SNSLPPVRSVLTQGTTAEKVQLVVSCLGVVCSIICLALGIAAAAVTAKRL VAVAVATILAVALLVVAGLLFSGVLCSPVSVLAASLFFGVGAFLLGGALV GGVLTTEAVTRERLHRSQTLMWNNLCCKTAEVEQKISTASANAKSNDKTR KLGE Seq 200 MECVKQLCRNHLCLDSLTGPVRSVLTQGTTAEKVQLVVSCLGVVCSIICL ALGIAAAAVGVSCSGFAIGLGVIAILLGIVLFAISALDVLEDHGLVGAAS LFFGVGAFLLGGALVGGCPFKLPCKSSPANEPTVQFFKGKNGSADKVILV TQ

TargetScan Find predicted targets of miRNA

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