GSS Assembly - Overview

Genome Survey Sequences (GSSs) comprise a bulk sequence division of GenBank. GSSs are in essence the genomic equivalent of ESTs. The GSS division contains first pass, single reads of genomic DNA. Typical GSS records are initial sequencing surveys and end reads of large insert clones from random or gene-enriched genomic libraries, exon-trapped genomic sequences, and Alu PCR sequences.

PlantGDB collaborates with Dr. Xiaoqiu Huang's group at ISU on the species-specific assembly of plant GSSs (currently all from maize and sorghum). The assembly is accomplished using PCAP. Sets of genes containing presumed full-length coding regions are identified by spliced alignment with presumed homologous proteins and tentatively annotated with gene-family and GO term information from the homolog, as available. All contigs can be searched using BLAST and downloaded in bulk.

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