Tag SNP and Singleton SNP

Tag SNP:

A group of SNPs in a region of a genome may be in high linkage disequilibrium (LD). In such case, one SNP, called a tag SNP, represents the whole group. As sequencing SNPs is costly, often only the tag SNP, instead of the all the SNPs in the group, is sequenced to find genetic variation that may be associated with a phenotype.

Singleton SNP:

Sometimes one tag SNP represents only itself i.e., it is not in high LD with any other SNPs in that region. Such tag SNP is called a singleton SNP.

References:

1) Wikipedia, Tag SNP, accessed on 29 March 2015.

2) Xiayi Ke et al. (2008), Singleton SNPs in the human genome and implications for genome-wide association studies, European Journal of Human Genetics, 16, 506–515.

Types of RNA

• mRNA: Messenger RNA. Encodes amino acids sequences.
• tRNA: Transfer RNA. Carries amino acids to ribosome during translation.
• rRNA: Ribosomal RNA. Makes up ribosomes.
• snRNA: Small Nuclear RNA (U1, U2, U4, U5, and U6).
• sRNA: Small RNA. Binds to protein or mRNA targets, and regulates gene expression.
• miRNA: Micro RNA. A family of sRNA that regulates gene expression in a sequence-specific manner.
• siRNA:  Small Interfering RNA.
• dsRNA: Double-Stranded RNA
• pre-mRNA: Precursor mRNA. Contains both exons and introns.
• mature mRNA: All introns removed.

Useful links describing Biology concepts

• Difference among chromosome, chromatin, and chromatid: link
• Reciprocal cross: wiki
• True breeding organism: wiki
• Genome imprinting: wiki, geneimprint
• Decoy sequence: biostars

Homologs, Orthologs, and Paralogs

Homologs, Orthologs, and Paralogs - these 3 terms are conceptually related. It is necessary to understand the distinction among them.

Homology means that two genes are related by descent i.e. they have a common ancestral DNA sequence. Homology can be divided into two parts - Orthology and Paralogy. Orthologs are results of speciation, while Paralogs are results of gene duplication.

Orthology and Paralogy can easily be determined from the ancestral tree. You have to track along the vertical line of descent and find the place where the pair of genes join. If they join at an upside-down 'Y' node, then they are orthologs. In contrast, if they join at a horizontally connected node, then they are paralogs.

Here is an example [1]. In Fig. (a):

• A1 has 5 Orthologs - B1, B2, C1, C2, C3, as all five orthologs join with A1 at an inverted 'Y' node, where speciation occurred.
• B1 & B2 are paralogs, as they meet horizontally, where gene duplication took place.
• B1 & C1 are orthologs.
• C1, C2 & C3 are paralogs to each other.

Fig. (b) and Fig. (c) are actually same. (c) is actually a detailed illustration of (b). Here:

• A1 & A2 (and also B1 & B2) are orthologs.
• A1 & B1; A1 & B2; A2 & B1; A2 & B2 are all paralogs.

Identification of orthologs can play a significant role to determine evolutionary history. Usually, orthologs have the same function as their common ancestor, while paralogs do not. Bioinformaticians often take advantage of this behavior to differentiate orthologs from paralogs. But, functional similarity (or dissimilarity) does not necessarily imply orthologs (or paralogs).

Reference:

1. Jensen,R.A. (2001) Orthologs and paralogs - we need to get it right. Genome Biol., 2(8). [link]

Other Sources:

1. http://homepage.usask.ca/~ctl271/857/def_homolog.shtml
2. http://biology.stackexchange.com/questions/4962/what-is-the-difference-between-orthologs-paralogs-and-homologs