What is EST in bioinformatics?
Abstract. Expressed sequence tags (ESTs) are fragments of mRNA sequences derived through single sequencing reactions performed on randomly selected clones from cDNA libraries. To date, over 45 million ESTs have been generated from over 1400 different species of eukaryotes.
What is EST in NCBI?
Expressed Sequence Tags (ESTs) are short (usually <1000 bp), single-pass sequence reads from mRNA (cDNA). Typically they are produced in large batches. They represent a snapshot of genes expressed in a given tissue and/or at a specific developmental stage.
What are STS and EST?
EST (expressed sequence tag): A unique stretch of DNA within a coding region of a gene that is useful for identifying full-length genes and serves as a landmark for mapping. An STS is a short segment of DNA which occurs but once in the genome and whose location and base sequence are known.
What is EST evidence?
In genetics, an expressed sequence tag (EST) is a short sub-sequence of a cDNA sequence. ESTs may be used to identify gene transcripts, and were instrumental in gene discovery and in gene-sequence determination. An EST results from one-shot sequencing of a cloned cDNA.
What is EST analysis?
ESTs are unique DNA sequences generated by sequencing cDNA clones from cDNA libraries. In the Sanger sequencing era, EST sequencing served as an important approach in identification and analysis of gene transcripts and expression (Adams et al., 1991).
What is a human EST?
The Expressed Sequence Tag (EST) division of Gen-Bank, dbEST, is a large repository of the data being generated by human genome sequencing centers. ESTs are short, single pass cDNA sequences generated from randomly selected library clones.
How does NCBI calculate est?
In the desired Gene record (such as for human CTRC), follow the UniGene or GEO Profiles links on the right side of the page. Upon clicking on UniGene, scroll down to the “EST Profile” link in the Gene Expression section.
What is EST mapping?
EST (cDNA) mapping refers to the mapping of EST (cDNA) sequence file to the reference genome base sequence by using its homology to identify the genomic position from which EST is derived and registering the EST (cDNA) feature at that position.
What is EST application?
ESTs have a wide range of applications. They provide an alternative to full-length cDNA sequencing. Also, ESTs are an inexpensive means of gene discovery. The randomly sequenced ESTs allow us to make gene discovery as they give information of the transcribed regions of the gene.
What is EST marker?
Expressed sequence tag-derived simple sequence repeat markers (EST-SSRs) are the markers of choice, because they are abundant, co-dominant, highly polymorphic, and are easily transferable among phylogenetically related species [13].
What is the difference between Blastn and Blastp?
The amino acid sequences being identical, blastp would have no problem in retrieving one sequence, using the other sequence as query. Blastn, however, uses a default word size of 11 nucleotides. This means the two sequences must match with at least 11 nucleotides for blastn to be able to report any hit at all.
What is EST SSR marker?
How are EST sequences represented in a database?
They may be represented in databases as either cDNA/mRNA sequence or as the reverse complement of the mRNA, the template strand . One can map ESTs to specific chromosome locations using physical mapping techniques, such as radiation hybrid mapping, Happy mapping, or FISH.
Which is the best definition of bioinformatics?
Bioinformatics: An absolute definition of bioinformatics has not been agreed upon. The first level, however, can be defined as the design and application of methods for the collection, organization, indexing, storage, and analysis of biological sequences (both nucleic acids [DNA and RNA] and proteins).
How are ESTs used to determine gene expression?
ESTs contain enough information to permit the design of precise probes for DNA microarrays that then can be used to determine gene expression profiles. Some authors use the term “EST” to describe genes for which little or no further information exists besides the tag.
Are there any high throughput analyses of ESTs?
High-throughput analyses of ESTs often encounter similar data management challenges. A first challenge is that tissue provenance of EST libraries is described in plain English in dbEST. This makes it difficult to write programs that can unambiguously determine that two EST libraries were sequenced from the same tissue.