Splicing is a biological phenomenon that removes the non-coding sequence from the transcripts to produce a mature transcript suitable for translation. To study this phenomenon, information on the intron-exon arrangement of a gene is essential, usually obtained by aligning mRNA/EST sequences to their cognate genomic sequences. MGAlign is a novel, rapid, memory efficient and practical method for ...

To enrich the genomic information of the commercially important fish species, we obtained 5,063 high-quality expressed sequence tags (ESTs) from the muscle cDNA database of the mandarin fish (Siniperca chuatsi). Clustering analysis yielded 1,625 unique sequences including 443 contigs (from 3,881 EST sequences) and 1,182 singletons. BLASTX searches showed that 959 unique sequences shared homolog...

Expressed sequence tag (EST) sequences can provide a wealth of data for phylogenetic and genomic studies, but the utility of these resources is restricted by poor taxonomic sampling. Here, we use small EST libraries (<1,000 clones) to generate phylogenetic markers across a broad sample of insects, focusing on the species-rich Coleoptera (beetles). We sequenced over 23,000 ESTs from 34 taxa, whi...

EST-derived simple sequence repeat markers (EST-SSRs) are important tools for studies on genetic diversity, phylogeny, evolution, comparative genomics, QTL analysis, and gene-based associations. We have searched the literature known EST-SSRs used Scots pine (Pinus sylvestris L.) – one of world’s major forest species. Then, 91 102 suggested were manually aligned against reference genome Pinus ta...

The yield of soybean (Glycine max L. Merr.) has been seriously challenged by increased salinization of the land. Continuous efforts are needed to understand the salt tolerance mechanism in soybean using suitable biotechnological tools. Although the suppression subtractive hybridization (SSH) method was a powerful technique and has been successful in some cases, it may retain some less effective...

In this study, a cDNA library was constructed from the total RNA of sweet potato leaves. A total of 789 copies of the cDNA were cloned in Escherichia coli by employing the pGEM-T Easy vector. Sequencing was carried out by Solgent Co. (Korea). As many as 579 expressed sequence tag-simple sequence repeat (EST-SSR) markers were designed (73.38%) from the known cDNA nucleotide base sequences. The l...

Expressed sequence tag (EST) sequencing projects are being undertaken in an effort to identify the function of as many genes as possible fmm entire genomes. Putative function can be determined by analyzing the similarity of the ESTs to sequences in the public databases. We are involved in a long-term project to research and develop database technology to store and analyze ESTs for Arabidopsis t...

Expressed sequence tags simple sequence repeats (EST-SSRs) are important sources for investigation of genetic diversity and molecular marker development. Similar to genomic SSRs, the EST-SSRs are useful markers for many applications in genetics and plant breeding such as genetic diversity analysis, molecular mapping and cross-transferability across related species and genera. In spite of low po...

We present evidence of cross-hybridization artifact intrinsic to spotted single-dye cDNA microarrays as a result of cDNA containing 5’-end sequences of consecutive thymidine (dT) residues. These poly(dT) tracts result from the synthesis, via oligo (dT) primed reverse transcription, of expressed sequence tags (EST) cDNA from a polyadenylated mRNA template. Analysis of gene expression data from t...

MOTIVATION Repeat sequences in ESTs are a source of problems, in particular for clustering. ESTs are therefore commonly masked against a library of known repeats. High quality repeat libraries are available for the widely studied organisms, but for most other organisms the lack of such libraries is likely to compromise the quality of EST analysis. RESULTS We present a fast, flexible and libra...