The sequence data maintained in public databases are available in heterogeneous formats like FASTA, XML, and ASN1. The XML representation of data is heterogeneous in nature with different DTD in various databases. The difference lies in the representation of sequence description as XML tags. The protein and genomic data in XML format in Genbank has more than 3500 tags to represent the functiona...

We describe a technique, sequence-tagged microsatellite profiling (STMP), to rapidly generate large numbers of simple sequence repeat (SSR) markers from genomic or cDNA. This technique eliminates the need for library screening to identify SSR-containing clones and provides an approximately 25-fold increase in sequencing throughput compared to traditional methods. STMP generates short but charac...

Peptide tags fused to proteins are used in a variety of applications, including as affinity tags for purification, epitope tags for immunodetection, or fluorescent protein tags for visualization. However, the peptide tags can disrupt the target protein function. When function is disrupted by fusing a peptide to either the N or C terminus of the protein of interest, identifying alternative ways ...

We analysed the publicly available expressed sequence tag (EST) collections for the genus Populus to examine whether evidence can be found for large-scale gene-duplication events in the evolutionary past of this genus. The ESTs were clustered into unigenes for each poplar species examined. Gene families were constructed for all proteins deduced from these unigenes, and K(S) dating was performed...

The National Institutes of Health Mammalian Gene Collection (MGC) Program is a multiinstitutional effort to identify and sequence a cDNA clone containing a complete ORF for each human and mouse gene. ESTs were generated from libraries enriched for full-length cDNAs and analyzed to identify candidate full-ORF clones, which then were sequenced to high accuracy. The MGC has currently sequenced and...

Although treatment manuals have existed for many years, controversy surrounds their use and dissemination. In a previous article, we addressed assets and liabilities of using empirically supported treatments (ESTs) in psychotherapy, as well as obstacles to disseminating such treatments. In this article, we argue that using EST aids clinical work and is ethically sound. At the same time, we draw...

Since a large number of computationally predicted exons are not supported by existing sequence (e.g. ESTs) or experimental (e.g. expression analysis) data they need to be validated by other methods. ETOPE is designed to test computational predictions by using signals that have not been included in any current computational prediction method. The test is based on the ratio of non-synonymous to s...

THE FIELD OF RESEARCH AND PRACTICE IN PSYCHOTHERAPY HAS BEEN DEEPLY INFLUENCED BY TWO DIFFERENT APPROACHES: the empirically supported treatments (ESTs) movement, linked with the evidence-based medicine (EBM) perspective and the "Common Factors" approach, typically connected with the "Dodo Bird Verdict". About the first perspective, since 1998 a list of ESTs has been established in mental health...

BACKGROUND Clustering is a key step in the processing of Expressed Sequence Tags (ESTs). The primary goal of clustering is to put ESTs from the same transcript of a single gene into a unique cluster. Recent EST clustering algorithms mostly adopt the alignment-free distance measures, where they tend to yield acceptable clustering accuracies with reasonable computational time. Despite the fact th...