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Related Concept Videos

Sequences01:29

Sequences

278
Sequences are fundamental mathematical objects consisting of ordered lists of numbers that follow a specific rule or pattern. Sequences are critical in various mathematical concepts, including calculus, series, and number theory. They can model real-world phenomena such as population growth, financial investments, and physical processes like the diminishing height of a bouncing ball.Each number in a sequence is referred to as a term. Typically, the terms are denoted as a1, a2, a3,…, where...
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Arithmetic Sequences01:30

Arithmetic Sequences

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An arithmetic sequence is a structured arrangement of numbers where each term is derived by adding a constant value, known as the common difference, to the previous term. This consistent pattern allows for the efficient computation of any term within the sequence as well as the cumulative sum of multiple terms. The formula for finding the nth term of an arithmetic sequence is:Here, aₙ represents the nth term of the sequence, a is the first term, d is the common difference, and n is the...
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Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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No description available
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Sanger Sequencing01:57

Sanger Sequencing

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DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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Next-generation Sequencing03:00

Next-generation Sequencing

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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
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TargetIdentifier: a webserver for identifying full-length cDNAs from EST sequences.

Xiang Jia Min1, Gregory Butler, Reginald Storms

  • 1Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec H4B 1R6, Canada. jack@gene.concordia.ca

Nucleic Acids Research
|June 28, 2005
PubMed
Summary
This summary is machine-generated.

TargetIdentifier is a web server that identifies full-length cDNA sequences from expressed sequence tag (EST) data. It uses BLASTX alignments to find protein-coding regions and assign functions to query sequences.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Expressed Sequence Tags (ESTs) are valuable for gene discovery but often require processing to identify full-length cDNA sequences.
  • Identifying protein-coding regions and translation start/stop codons within EST data is crucial for accurate gene annotation.
  • Existing methods may not efficiently integrate sequence alignment and functional prediction for EST-derived contigs and singletons.

Purpose of the Study:

  • To introduce TargetIdentifier, a novel web server designed for the identification of full-length cDNA sequences from EST data.
  • To provide a tool that accurately locates protein-coding regions and determines the presence of start codons in EST-derived sequences.
  • To enable the assignment of putative functions to query sequences using computational approaches.

Main Methods:

  • Utilizes BLASTX alignments to guide the identification of protein-coding regions within EST-derived contigs and singletons.
  • Employs algorithms to detect potential start and stop codons, assessing the completeness of identified coding regions.
  • Integrates BLASTX output for the functional annotation of processed sequences.

Main Results:

  • TargetIdentifier successfully identifies full-length cDNA sequences from EST data.
  • The tool accurately pinpoints protein-coding regions and translation start/stop codons.
  • Putative functions are assigned to query sequences based on BLASTX alignments.

Conclusions:

  • TargetIdentifier offers an efficient and reliable web-based solution for processing EST data.
  • The server aids researchers in gene discovery and functional genomics by providing annotated full-length cDNA sequences.
  • This tool enhances the utility of EST datasets for downstream biological research.