UK Bioinformatics Studentship Available

Dr D T Jones bssbc at
Fri Mar 14 11:33:41 EST 1997




Applications are invited for a BBSRC Special Studentship on
the application of hidden Markov models (HMMs) to genomic
fold recognition. This project would suit graduates in
biological sciences with a good knowledge of, or interest in
computing, or alternatively graduates from physical sciences
(e.g. physics, maths or computing) who now wish to apply
their skills to biological problems.

The research would be carried out in the Protein Structure Group
under the supervision of Dr David Jones. For details on the
Protein Structure Group, please check the following Web page:


This project would be directed at exploring the use of threading algorithms
for genomic analysis. Obviously the important question here is how many
folds can be recognised in large volumes of sequence data, and whether this
can be used to assign functions to gene products which cannot be assigned by
simpler methods. The basic idea that would be explored is how methods based
on Hidden Markov Methods (i.e. 1-D methods) could be combined with threading
methods (i.e. 3-D methods). The simplest approach to this would be to take
alignments generated from Hidden Markov Models (HMMs), though taking into
account, for example, gap restrictions based on the known structure and post
process the inferred model by means of empirical pair and solvation
potentials. We have already found this to be effective even when simple
pairwise sequence alignments are used as input, and the additional
sensitivity and accuracy of HMM alignments can only improve matters. This
approach should allow very fast screening of genomic data, whilst extending
the range of normal HMMs towards the recognition of extremely remotely
related folds.

As this is a BBSRC Special Studentship, a higher than normal stipend
of (currently) 6680 UK pounds per annum is payable.

PLEASE NOTE: Eligibility

1. The candidate should have a reasonable background in computing,
and a 1st or upper second class honours degree (or equivalent).

2. The candidate must be a UK Citizen who has been ordinarily resident
in Great Britain or N. Ireland throughout the three year period upto the
date of application. No period of the candidate's residence during those
three years should have been wholly, or mainly, for the purpose of full time

For general information about the Department of Biological Sciences,
please browse the following address:

Dr David T. Jones
Address: Dept. of Biological       |   Email: jones at
Sciences, University of Warwick,   |     Tel: +44 1203 523729
Coventry CV4 7AL, U.K.             |     Fax: +44 1203 523701

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