Kinetoplast Kristmas

[Al Ivens]

Dear Colleagues,

The PSU at the Sanger Centre are happy to announce the deposition of a
large wudge of kinetoplast DNA sequence in the EMBL database.

***  T. brucei  ***
T. brucei home page: http://www.sanger.ac.uk/Projects/T_brucei/
T. brucei Genome Network home page: http://parsun1.path.cam.ac.uk/

43,196 new GSS sequences were submitted to EMBL late this week, and
should be available on Monday for public access
(http://www.ebi.ac.uk/Databases/index.html).  Access from GenBank should
be possible within ~ a week's time
(http://www.ncbi.nlm.nih.gov/Entrez/nucleotide.html).  

However, for speedy access right now, a gzipped fasta database of these
sequences is available from our ftp site:

ftp://ftp.sanger.ac.uk/pub/databases/T.brucei_sequences/GSS/

A list of accessions and IDs is also provided on the ftp site.  The GSS
have not yet been placed in the T. brucei blastserver database, but will
be in the New Year.  The GSS sequences are currently being BLASTX'ed
against Swissprot/TrEMBL, and the top hits from the first batch of ~3600
GSS seqs can be found at: 

http://www.sanger.ac.uk/Projects/T_brucei/0001Blasthits.html

Additional BLASTX hit data will be put on the www, as and when they are
completed.


***  L. major  ***
L. major home page: http://www.sanger.ac.uk/Projects/L_major/
Leishmania Genome Network home page:
http://www.ebi.ac.uk/parasites/leish.html

Several cosmid and PAC sequences have been returned by members of the
EULEISH consortium, and submitted to EMBL.  They are:

Final sequence, reannotation
LMFP1408      109,041 bp AL358652
LMFL2185       35,424 bp AL358712
LMFL5856       23,600 bp AL357592
LMFL6754       15,121 bp AL358632
LMFL5852       31,392 bp AL499614

Final, new sequence, annotated
LMFL4766       26,122 bp AL499615

Pre-final, new sequences, not annotated yet
LMFL9356       23,973 bp AL499612
LMFL4812       33,109 bp AL499613
LMFL490        29,151 bp accesssion not received yet
LMFL654        19,179 bp accesssion not received yet
LMFP696       176,944 bp accesssion not received yet

In addition, the PSU has been doing a large number of whole chromosome
shotguns (WCS) of PFG-purified Leishmania chromosomes, plus "skims" of
suitable mapped cosmids and/or PACs.  

A ***preliminary*** assembly of these has been done, and all sequence
contigs greater than 500bp submitted to EMBL.  Shotgun is *not*
completed for the majority, these are still work-in-progress:
HTGS_PHASE1.

PLEASE NOTE THAT THESE SEQUENCES HAVE NOT BEEN EDITED AT ALL AND SHOULD
BE USED WITH CAUTION!!!

LMFLCHR25  AL499618  Chromosome 25, 667 contigs, 918,546 bp
LMFLCHR16  AL499619  Chromosomes 16&17, 800 contigs, 1,030,105 bp
LMFLCHR18  AL499620  Chromosomes 18&19&20&22, 721 contigs, 1,091,246 bp
LMFLCHR31  AL499621  Chromosome 31, 616 contigs, 1,027,083 bp
LMFLCHR32  AL499622  Chromosomes 32&33, 1737 contigs, 2,727,709 bp
LMFLCHR34  AL499623  Chromosome 34, 654 contigs, 697,361 bp
LMFLCHR36  AL499624  Chromosome 36, 1511 contigs, 1,650,993 bp

It should also be noted that some cross-contamination between
PFG-isolated chromosomes does occur, although we have endeavoured to
maximise chromosome purity prior to library construction.  

Data from chromosomes 15, 26 and 28 have been available for some time,
and can be found on their respective www pages, e.g.:

http://www.sanger.ac.uk/Projects/L_major/chromosome15.shtml
http://www.sanger.ac.uk/Projects/L_major/chromosome26.shtml
http://www.sanger.ac.uk/Projects/L_major/chromosome28.shtml

On my return in the New Year, a low-level annotation will be performed
on the new WCS, and resubmitted.

Wishing you all a Happy Christmas and New Year, I'm off to snowy
Scotland now!

Cheers!

al


==================================
Al Ivens
Pathogen Sequencing Unit
Sanger Centre
Wellcome Trust Genome Campus
Hinxton
Cambs. CB10 1SA
UK

Tel -44-1223- 49 48 51
Fax -44-1223- 49 49 19
Email: alicat at sanger.ac.uk