Help

Getting started with a sequence (gene)
Getting started with an organism
Configure organism views
Navigate the transcriptome browser
Tooltips information
Gene page
Multi-track view of homologs
BLAST (access homolog transcriptomes with sequence query)

General notes:

All features of our coverage plot viewer are supported on Chrome and Firefox browsers.
It is therefore advised to use TCOL on either Chrome or Firefox.

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Getting started with a sequence (gene)

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Use BLAST to find the homologs in our data and follow the links to their transcriptomes

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Getting started with an organism

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• Microbes spanning the Tree Of Life - Access one of 18 organisms across 7 phyla.
  
  
   

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Configure organism views

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• "Replicon (Accession)" - Genome or plasmid (toggle).
  
  
   


• "Condition" - choose growth conditions (multiple tracks can be viewed comparatively).
  
  
   

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Navigate the transcriptome browser

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• "Position" - type genome coordinates, and "Go" (aligned in center).
  
  
   


• "Genes" - type gene name (first couple of letter prompt the completion list)
  Alternatively use arrow buttons "<" ">" .
  
  
   


• "Rfam sRNAs" - type sRNA name (first couple of letter prompt the completion list)
  Alternatively use arrow buttons "<" ">" .
  
  
   


• "Rfam Cis regulators" - type Cis regulator name (first couple of letter prompt the completion list).
  Alternatively use arrow buttons "<" ">" .
  
  
   

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Tooltips information

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Tooltips appear when pointer (cursor) hover above element


• "Gene" - Locus name, Gene name (if available), coordinates.
  
  
   


• "Transcription Start Site (TSS)" - Pos (coordinate), Reads (# 5' mapped reads), Score (reliability of TSS, on 0-1 scale).
  
  Primary TSS (high score)
  
  
   
Alternative TSS (low score)


 

• "Coverage" - Pos (coordinate), Reads (# mapped reads).
  
  
   


• "Operon" - Coordinates, Operon number, number of genes.
  
  
   


• "Rfam genes" - Type (CIS regulator or sRNA gene), Coordinates, Gene name, RFAM accession, description.
  
  
   

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Gene page

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• "Click on Gene to access" - appears as separate page.
  
  
   


• "Current gene info" - Locus GI Prot ID Gene name Product description 5UTR length Expression level (RPKM) Antisense proportion View of raw data.
  
  
   


• "View of raw data" - Multi-track view of locus with: A. integrated (high confidence TSSs) B. TAP (treated lib) C. NoTAP (untreated lib)
  
  
   


• "Additional information resources for locus" - re-direction to various Genomic resources.
  
  Link to KEGG entry - useful to obtain details about:
  pathway involvement, function, and sequence (Amino Acids, Nucleotides, including upstream and downstream which can be used for extracting 5’UTR sequences).
  Link to STRING entry - study the network of related genes by Neighbourhood, Co-occurrence, Co-expression, Experiments (protein interactions) etc.
  Link to Protein information at NCBI GenPept
  Link to BacMap entry - view locus with adjacent neighbouring genes
  
  
   


• "Comparative view of top homologues genes" - Multi-track view of homologs (see more details in section below).
  
  Comparative viewer presenting multiple tracks containing homologues genes (Best Bi-directional Hits)
  
  
   


• "Table of all homologues genes" - Table of homologues genes (transcriptome information of homologs).
  
  Homologues genes are defined as Best Bi-directional Hits.
  Links to the transcriptome are depicted for each homolog gene in the table.
  
  
   


• "COG-based homology" - The family members are depicted by COG (Clusters of Orthologues Groups) classification.
  Three COG-levels are available:
  1. TOL (Orthologues groups across the Tree Of Life).
  2. Domain (Domain-specific orthologues groups, Bacteria or Archaea).
  3. Phylum (Phylum-specific orthologues groups)..
  
  Links to the transcriptome are depicted for each homolog gene in the table.
  
  
   

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Multi-track view of homologs

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• "Comparative viewer" - aligned transcriptomes of orthologs (all BBH to chosen locus).
  
  In this example, the first locus is phenylalanyl-tRNA synthetase from Clostridium, and we show the comparative viewer with the strongest 3 orthologs .
  
  
   

In the comparative transcriptomics viewer with Multi-track view of different organisms you can scroll each genome to a specified genomic coordinates.
For this, first choose the 3-letter KEGG organisms code (these are ordered top to bottom the same as the comparative viewer order).
Then, fill-in the required genomic position in the Position text field and press enter.

 

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BLAST (access homolog transcriptomes with sequence query)

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• "BLAST" - use either protein or DNA sequences.
  
  In this example, we show blastp (Amino acids query against all proteins in our compendium) .