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Transterm

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Introduction

Welcome to Transterm 2008, a database providing access to mRNA sequences and associated regulatory elements.

The mRNA sequences are processed from Genbank, including complete genomes. They are divided into biologically relevant sections 5' UTRs and 3' UTRs, initiation and termination regions and the full CDS sequences.

This data or your own sequences can be searched for defined regulatory elements (e.g. Puf3, Iron Responsive Element)

A more detailed overview is found in our recent publication "Transterm: a database to aid the analysis of regulatory sequences in mRNAs"in Nucleic Acids Research.

What can be done here?

Obtain data relating to translation, by species in a non-redundant format: for example bias around initiation and termination codons, or codon usage (more...).

Search for regulatory elements in a defined set - for example known or putative mRNA stability or localisation elements in 3'UTRs (more...).

Search your own sequence for known regulatory elements (more...).

Quick guide - how to use the database

This database contains data related to specific species and strains through NCBI TaxIDs, the initial default is Homo Sapiens (9606).

1) For the species many types of pre-processed data are available, differing in experimental support and redundancy. For completed genomes the most useful files are likely to be 'NCBI-Genomes - one sequence for each coding region' (more...)

2) Choose your TaxID species or strain (example...).

3) This data can be analysed for known or putative regulatory elements (more...). More about regulatory elements in mRNAs.

Alternative ways of using the database

Get descriptions of regulatory elements (example...).

Search the data using BLAST (search).

A question based approach to the database. How can I ...? (more...).

Datasets by ftp (ftp).

Previous version of the interface and data (TT2007).

Results

The results of your analysis will appear in a new tab or window (more...).

 

1. Database, species, file :

Choose a database:
Select sequence category:
Enter NCBI TaxID for species or strain: Homo sapiens
  Examples: 9606 H. Sapiens, 3702 A. thaliana, 7227 D. melanogaster, 316407 E. coli K12 W3110, 208964 P. aeruginosa PAO1 more...
Select data file:

Preview and download data:

Preview data and email it (new window)   Download data   List of all the files available (new window)
         

2. Search for regulatory elements in specific regions:

Start codon ...

... coding region ...

... stop signal
                                   
                 
  Init. region       Term. region  
         
     
          CDS          
                   
     
  5' flank           3' flank  
             
Search  Non-redundant sequences (criteria) or  all sequences.

3. Or search your own sequence for regulatory elements

Note: The default search is for those patterns without 'False positive' warnings: 

Use FASTA format, max. size 30,000 e.g.:
> My mRNA
ATTGGTTTA....
Search program to use:

Alternatively use BLAST (search).
Transterm regulatory element   List all
OR  Enter your own pattern   
  Last modified: 17 Feb 22:49:45 2009 (TTDB)