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tRNA search (HELP)

Uttam Rajbhandary bhandary at wccf.mit.edu
Fri Jul 1 19:07:00 EST 1994


In article <1994Jun21.173724.1 at ugsc2a>, otello at sc2a.unige.ch writes...
>Dear netters:
> 
>I would like to know if anybody out there knows of a method
>to detect putative tRNA sequences in a given nucleotide sequence.
>I have an 900 bp sequence in which somebody mapped a tRNA a while ago,
>and I would like to verify if it is really there, since I plan some mutagenesis
>in this fragment.
> 
>Thanks a lot in advance

There is an old Zucker program that will give putative tRNAs from a sequence.  
However, one must be aware of some basic "rules of thumb" to intrepret the 
output reasonably.  For example:
1. acceptor stem has seven base pairs
2.  Anticodon stem has 5 basepairs
3.  anticodon loop as 7 nucleotides: two pyrimidines on the 5', two purines on 
the 3'; three base anticodon.  If yeast, fungi, watch out for intervening 
sequences.
4.  T stem has 5 base pairs; 5 bases in the loop;  the sequence GTTCPu should 
appear at the begining of this loop (unless a eukaryotic initiation: GATCPu.
If position 54 is T, then position 60 should be T or C.
5.  If bacterial, the CCA will be encoded.  If eukaryotic, it won't be; expect 
the gene to be bounded on the 3'-side past the descriminator base by a run of 
T's.

These are guides; MOST tRNAs will fit; but not all.

The Zucker program uses an algorithm to find base pairing of 7 nucleotides to 
another 7 nucleotides located an appropriate distance downstream.  Then it 
starts to apply other criteria (T stem/loop size, etc.); it only filters on 
the specific bases if you pick that option. However,it is a big help to scan a 
large sequence.  I know the program runs on VAX; other platforms may be 
available.  In the meantime, you might be able to use what I have listed above 
to eyeball it, especially if it's eukaryotic (find the oligo-T).


Harold Drabkin
c/o Bhandary at wccf.mit.edu




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