Wheat EST Assembly

The EST contig assembly is done using the software program phrap.

Global EST assembly

The first round of global EST contig assembly was carried out on Jan 29, 2001 included about 60,000 5' ESTs. Among them over 39,000 have been clustered and assembled into 7929 contigs. Among 7929 contigs, 6900 have at least two members of ESTs clustered in the contigs. The parameters used for assembly were -penalty -5 -minmatch 50 -minscore 100.

The second round of global phrap assembly was done on April 1, 2002 including 77,022 triticeae ESTs generated in this project so far. Among 77,022 ESTs used for new assembly, 70,074 were 5' ESTs, 6,948 were 3' ESTs, and they were assembled into 11,758 contigs. 18,903 ESTs were remained as singletons. Altogether, the number of triticeae unigenes is now at 30,661. The parameters used for this round of assembly were -penalty -5 -minmatch 50 -minscore 75.

The latest global phrap assembly was done on January 8, 2003. This new assembly has included all the ESTs generated from this project. Altogether 117,510 ESTs were included, among them 101,912 were 5' ESTs and 15,598 were 3' ESTs. The new assembly has yielded 18,876 contigs and 23,034 singletons. The parameters used were -penalty -5 -minmatch 50 -minscore 100.

To query contig information from all versions, please go to GrainGenes-SQL page.

EST assembly within a library

EST assembly was carried out for each individual libraries to assess the level of library redundancy. The results can facilitate the decision on deep sequencing of particular cDNA libraries. The results from global assembly have been used to estimate the extent of ESTs unique to a specific library. To view the summarized results, please go to the library redundancy table. The parameters used are -penalty -5 -minmatch 50 -minscore 100.