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tRNA search

This method is used to find segments of a sequence that might code for tRNAs. It looks for potential cloverleaf forming structures and then for the presence of expected conserved bases. It presents results graphically and draws out the cloverleafs. A large number of parameters need to be given values, including some loop lengths, scores for each of the four stems, and scores for the conserved bases. But we have not yet included an interface for setting these! The algorithm was first described in Staden,R. (1980) A computer program to search for tRNA genes. Nucl. Acid Res 8, 817-825, but has been completely rewritten since then. The tRNAs that have been sequenced so far have two characteristics that can be used to locate their genes within long DNA sequences. Firstly they have a common secondary structure - the cloverleaf - and secondly, particular bases almost always appear at certain positions in the cloverleaf. The cloverleaf is composed of four base-paired stems and four loops. Three of the stems are of fixed length but the fourth, the dhu stem which usually has four base pairs, sometimes has only three. All of the loops can vary in size. The following relationships between the stems in the cloverleaf are assumed in the program: (a) there are no bases between one end of the aminoacyl stem and the adjoining tuc stem; (b) there are two bases between the aminoacyl stem and the dhu stem; (c) there is one base between the dhu stem and the anticodon stem; (d) there are at least three bases between the anticodon stem and the tuc stem. The program looks first for cloverleaf structure and then, if required, for conserved bases. The sizes of the loops, the number of basepairs in the stems and the required conserved bases may all be specified by the user. The process of looking for the presence of conserved bases can reduce the number of potential structures found considerably. The user may also specify that an intron may be present in the anticodon loop. The output shows the position of the possible gene in the sequence by a vertical line the height of which shows the number of basepairs made in the stems. Typical graphical output:

[picture]
(Click for full size image)

The cloverleaf structure is also drawn in the text output window. Typical text output:

[picture]
(Click for full size image)


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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/nip4_28.html