Wheat SNP Development!
Peter Isaac, Organizer
Last update 1 December 2003
The wheat breeding and research community would benefit from coordinating
its efforts to develop SNPs in wheat, to ensure that the alignments of ESTs
are exploited to the full with minimum duplication of effort between
The Wheat SNP Development project aims to facilitate this coordination.
This is a public project, and all work done will be accessible and in the
public domain. The effort is open to all groups to participate.
There is an email discussion group for participants. To be included, contact firstname.lastname@example.org.
- General modus operandi
- 12 December 2002 (Build 3) -- includes the
Dupont ESTs. 410,000 ESTs total. Statistics.
- 28 October 2002 (Build 2) -- More overassembled, 90% identity instead of 95%.
- 20 June 2002 (Build 1)
- Super Plums, 20 Jan 03 -- the 1168 biggest contigs are now being allocated!
Groups now participating: Azanza, Balyan, Berry, Blake, Buerstmayr, Henry,
Isaac, Korzun, Laforest, See, Somers, Stephenson.
- Plums -- the 5343 contigs that contain seven or more ESTs
- Apples -> Oranges -- Translation of the EST names to their corresponding GenBank accessions.
- The Whole Thing -- including singletons. File "0.WheatAssembly.20jun2002.tar.gz", 15MB. 200MB uncompressed.
- CONTIG Database -- includes results of BLAST against GenBank. Example.
- Browse the whole directory -- 23,000 contig files, all alike (slow)
- Nomenclature -- the (old) coding system used to name the ESTs and contigs
- Software Updated, 1 Dec
- Genotypes and seed stocks
- Validation methods
- Reports -- Example
- SNP nomenclature proposal
Resources for SNP discovery
- New! 1 Dec SNPF, Single Nucleotide Polymorphism Finder
From Daniel Nwankwo, John Innes Centre.
- AutoSNP [ Top page | Example SNP report ]
More than 3300 SNP-containing clusters from an assembly of 132,000 wheat ESTs.
From cerealsDB at IACR-LARS.
- Jalview [ Server ]
A tool for viewing and manipulating contig alignments to extract SNPs by eye.
From Michele Clamp, EBI.
A Perl script to convert CAP3's ".cap.ace" output to padded-FASTA format.
(Only one contig at a time.)
- Other wheat EST assemblies
A database to compare assemblies vs. each other.
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