Barley Expression Database
Go Top Menu

What is the Cluster Viewer?

The cluster viewer displays a group of contigs and singlets as a cluster in which computationally predicted components from same locus are gathered. Basically a contig composed of only 5' EST have one partner contig composed of 3' EST, in which mate paired 5' EST and 3' EST from a same clone in the cDNA library are separated into each contigs respectively and which are expected to come from same locus. We call such a set of contigs and singlets sharing mate paired ESTs as a cluster and we predict a cluster correspond a gene locus. However, in many cases, a cluster composed of not only a 5' contig and a 3' contig but some other contigs and singlets, which expected to be caused by splicing variance, biological or experimental fluctuation noise or miss assembling of sequences from homologous genes. On the contrary, it is possible 5' contig and 3' contig sequentially connect into one contig in case an original gene is short. In such a case, a cluster composed of only one contig.

Explanation of the header

The header of Cluster Viewer includes the cluster ID of this cluster (CL1004), number of contigs in the cluster (Contig: 3), number of singlets in the cluster (Singlet: 1), number of 5' ESTs in the cluster (EST(5'): 26) and number of 3' ESTs in the cluster (EST(3'): 25).

Explanation of the table

On the below table includes all components in the cluster, which are contigs (AsmblUn458-Contig1-1, AsmblUn458-Contig2-1 and AsmblUn458-Contig3-1) and singlets (NIASHv1021L08_F.ab1). Because a contig composed of several 5' ESTs and/or several 3' ESTs, the number of 5' ESTs and the number of 3' ESTs are displayed on this table. You can download sequence files as the following three type of format if you click links "~KB" on the right side of the table.

Download File Type Explanation
Consensus sequences A single FASTA format of a consensus sequence of the contig.
EST Multi FASTA A multi FASTA format including all FASTA entries of composing ESTs.
Alignment File A customized format of multiple alignments of the contig.