Unigenes: Difference between revisions

Revision as of 15:45, 9 February 2025

Unigenes

Unigenes are a concept in genomics and bioinformatics that refer to a unique sequence of DNA that represents a single gene. The term is often used in the context of gene expression studies and genome annotation.

Overview

Unigenes are constructed by clustering expressed sequence tags (ESTs) and other cDNA sequences to form a non-redundant set of gene-oriented clusters. Each unigene cluster represents a unique gene locus, which can be used to study gene expression patterns across different tissues and conditions.

Applications

Unigenes are widely used in functional genomics to identify and annotate genes in newly sequenced genomes. They provide a valuable resource for comparative genomics and can help in identifying orthologs and paralogs across different species. Additionally, unigenes are instrumental in the development of microarrays and other high-throughput technologies for studying gene expression.

Construction

The construction of unigenes involves several steps:

1. **Collection of ESTs**: Large-scale sequencing projects generate ESTs from various tissues and developmental stages. 2. **Clustering**: ESTs are clustered based on sequence similarity to form groups that represent a single gene. 3. **Assembly**: Within each cluster, sequences are assembled to create a consensus sequence, which is the unigene. 4. **Annotation**: The resulting unigenes are annotated with functional information, such as gene ontology terms and pathway associations.

Challenges

One of the main challenges in unigene construction is the presence of alternative splicing, which can result in multiple transcripts from a single gene. This can complicate the clustering and assembly process. Additionally, sequencing errors and polymorphisms can affect the accuracy of unigene representation.

Related pages

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-'''Unigenes''' are a type of [[genetic sequence]] that are unique in a specific [[genome]]. They are derived from [[expressed sequence tags]] (ESTs) and are used in [[genomics]] and [[bioinformatics]] to identify and study genes. Unigenes are a crucial resource for gene discovery, [[gene mapping]], and the development of [[molecular markers]].
+== Unigenes ==
+[[File:Unigenes_humifusa_342167844.jpg|thumb|Unigenes humifusa]]
+'''Unigenes''' are a concept in [[genomics]] and [[bioinformatics]] that refer to a unique sequence of [[DNA]] that represents a single gene. The term is often used in the context of [[gene expression]] studies and [[genome annotation]].
 == Overview ==
-Unigenes are assembled from [[cDNA libraries]], which are collections of [[cDNA]] sequences derived from the [[mRNA]] of a specific organism or tissue. The process of unigene creation involves several steps, including [[sequence alignment]], [[clustering]], and [[consensus sequence]] generation. The resulting unigenes represent a non-redundant set of gene-oriented clusters.
+Unigenes are constructed by clustering [[expressed sequence tags]] (ESTs) and other [[cDNA]] sequences to form a non-redundant set of gene-oriented clusters. Each unigene cluster represents a unique gene locus, which can be used to study gene expression patterns across different tissues and conditions.
 == Applications ==
-Unigenes are used in a variety of applications in genomics and bioinformatics. They are used in [[gene discovery]], as they can provide a comprehensive view of the genes expressed in a particular organism or tissue. Unigenes are also used in gene mapping, as they can be used to identify the location of genes on [[chromosomes]]. In addition, unigenes are used in the development of molecular markers, which are used in [[genetic mapping]] and [[marker-assisted selection]].
+Unigenes are widely used in [[functional genomics]] to identify and annotate genes in newly sequenced genomes. They provide a valuable resource for [[comparative genomics]] and can help in identifying [[orthologs]] and [[paralogs]] across different species. Additionally, unigenes are instrumental in the development of [[microarrays]] and other [[high-throughput]] technologies for studying gene expression.
-== Databases ==
+== Construction ==
-Several databases exist that store and provide access to unigene data. These include the [[National Center for Biotechnology Information]] (NCBI) Unigene database and the [[European Bioinformatics Institute]] (EBI) ArrayExpress database. These databases provide researchers with access to a wealth of unigene data, facilitating research in genomics and bioinformatics.
+The construction of unigenes involves several steps:
+. **Collection of ESTs**: Large-scale sequencing projects generate ESTs from various tissues and developmental stages.
+. **Clustering**: ESTs are clustered based on sequence similarity to form groups that represent a single gene.
+. **Assembly**: Within each cluster, sequences are assembled to create a consensus sequence, which is the unigene.
+. **Annotation**: The resulting unigenes are annotated with functional information, such as [[gene ontology]] terms and [[pathway]] associations.
 == Challenges ==
-Despite their utility, unigenes present several challenges. The process of unigene creation is computationally intensive, requiring significant computational resources. In addition, the quality of unigenes can be affected by the quality of the input cDNA sequences. Errors in the cDNA sequences can result in errors in the resulting unigenes.
+One of the main challenges in unigene construction is the presence of [[alternative splicing]], which can result in multiple transcripts from a single gene. This can complicate the clustering and assembly process. Additionally, sequencing errors and [[polymorphisms]] can affect the accuracy of unigene representation.
+== Related pages ==
+* [[Gene expression]]
+* [[Expressed sequence tag]]
+* [[Genome annotation]]
+* [[Functional genomics]]
 [[Category:Genomics]]
 [[Category:Bioinformatics]]
-[[Category:Genetic mapping]]
-{{genetics-stub}}