New 'sequence tagged insert' Blast server at NASC / AGR

Sean May [ NASC ] sean_may at thale.life.nottingham.ac.uk
Thu Jun 22 09:53:45 EST 2000


Sequences derived from regions flanking transposon insertions
(colloquially referred to as 'sequence tagged inserts' or 'insert
sequences') are powerful tools for reverse genetics.

Simple searches of insert sequences against the sequence of your gene can
provide you with a potential mutant line, possibly a gene-function
'knockout'. Inspection of the sequence will also indicate where the
insertion sits within the gene itself (e.g promoter; intron; exon; 3'UTR).

This is the 'next step on' from PCR pool-hybridisation approaches for
reverse genetics and will become increasingly useful as the available data
on inserts expands to cover more of the genome / transcriptome.

A second use for sequenced inserts in this post-genomic phase of
Arabidopsis research is to provide 'launchpads' for local transposon
saturation of the area around the insertion. This is possible from
inspection of the 'Blast' derived genome position for the insert and the
transient re-introduction of a transposase source.

The NASC website now allows you to 'Blast' search against all public
Arabidopsis sequence tagged inserts. The results of your search are then
linked directly into the NASC stock catalogue to facilitate easy ordering
of your chosen potential knockout(s).

See: http://arabidopsis.org.uk/blast.html

Currently you can search against SINS (Sainsbury Laboratory, Jonathan
Jones' group, UK) and ITS (CPRO, Pereira Lab, Holland) sequences. In the
near future we will also include sequence information from the Launchpad
lines (John Innes, Paul Muskett, UK) and the IMA lines (IMA, Venkatesan
lab, Singapore).

Germplasm is already available at NASC for the SINS and IMAs and will
shortly be available for the Launchpad lines (also to be available at
ABRC) and Pereira insert lines.

In addition you can keyword search pre-computed blast results of all SINS,
IMA and ITS sequences searched against EMBL. This will find inserts based
on a variety of keywords including specific genes, BACS, gene families or
putative functions.

The Arabidopsis Genome Resource (AGR - http://ukcrop.net/agr/) now
contains improved information concerning insert sequences (IMA, SINS, and
Pereira ITS) and provides direct links to our resources for searching
insert homology information at NASC as described above.  Please see
http://ukcrop.net/agr/insert.html for more details.

AGR provides positional information about the local genome surrounding the
insertion of choice, and displays the insert position graphically in
relation to the gene structure.

AGR will contain new and updated insert information as soon as it becomes
available and is actively developed as a genome / map-oriented
complementary resource to the NASC germplasm catalogue.

Please address enquiries as below:
NASC catalogue: jamie at nasc.nott.ac.uk
AGR / genomics: keith at nasc.nott.ac.uk
Germplasm : karen at nasc.nott.ac.uk
General: arabidopsis at nasc.nott.ac.uk or sean_may at nasc.nott.ac.uk

All enquiries, donations of germplasm or 'insert sequences' are welcome.
If you are aware of tagged sequence insertions that could be made
available to the Arabidopsis community, please do contact
sean_may at nasc.nott.ac.uk to explore how we might improve this resource.



--------------------------------------------------------
Sean_May at nasc.nott.ac.uk
Director, Nottingham Arabidopsis Stock Centre (NASC)
Biological Sciences building, University Park,
Nottingham University. U.K. NG7 2RD.

FON:			+44 (0)115 9513237
FAX:			+44 (0)115 9513297
Catalogue:		seeds.arabidopsis.org.uk
Genomics:		ukcrop.net
Transcriptomics:	garnet.arabidopsis.org.uk
ICQ:			57288800


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