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 A bioinformatics tool for

the detection of mi-RNA in human genome 

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What is done? MicroRNAs (miRNAs) are evolutionarily conserved, small,

noncoding RNA molecules that regulate gene expression at

the level of translation

Mature microRNAs (miRNAs) are a class of naturally

occurring, small non-coding RNA molecules, about 21–25

nucleotides in length.

Hundreds of miRNAs have been identified by direct cloning

and computational approaches in several species.

All available miRNAs tools were web based; therefore aim of project was to provide the desktop access to scientist so that

they can easily make alignment of their sequences with

already discovered miRNAs without using internet.

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Contd. The aim and objectives in developing Mi-Discoverer were:

To provide desktop software tool facility to young scientist

Software in which there is facility of finding out new miRNAs

and saving,editing and searching the record of discovered

miRNA.

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What is the input? miRNA data includes names of miRNA in human genome, their

accession numbers, precursor sequences, precursor length,

mature sequences, mature length and different functions

perform by different miRNAs.

bioinformatics tools and databases used are miRanda,

miRDB,MiRNAMap, MicroInspector, MiRGen, MicroRNAdb,

Argonaute 2,MiRNAminer, PicTar, miRBase and Reference set

(The miRNAs and their precursor sequences were downloaded

from the MicroRNA Registry

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Comparing with some existing microRNA databases, miRNAdbprovides a more complete collection and full annotation: it contains allup-to-date reported microRNA genes and experiment validated targetmRNAs from all the 10 eukaryotic organisms and the 1 virus for whichmicroRNA have been reported, as well as references, expression data,genome location and some other detailed annotations.

 Argonaute 2 Database is a comprehensive database on mammalianmiRNAs and their known or predicted regulatory targets. It providesinformation on origin of miRNAs, tissue specificity of their expressionsand their known or proposed functions, their potential target genes as

 well as data on miRNA families based on their co-expression andproteins known to be involved in miRNA processing.

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The miRBase database is a searchable database of published miRNA sequencesand annotation

PicTar is an algorithm for the identification of microRNA targets. Thissearchable website provides details (3' UTR alignments with predicted sites,

links to various public databases etc) The miRNA Registry provides a service for the assignment of miRNA gene

names prior to publication. A comprehensive and searchable database of published miRNA sequences is accessible via a web interface(http://www.sanger.ac.uk/Software/Rfam/mirna/), and all sequence and

annotation data are freely available for download

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Basic information about entities DNA — is a nucleic acid that contains the geneticinstructions used inthe development and functioning of all known living organisms (withthe exception of RNA viruses). The main role of DNA molecules is thelong-term storage of information.

DNA consists of two long polymers of simple units called nucleotides, with backbones made of sugars and phosphategroups joinedby ester bonds and are antiparallel.

 

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rna RNA is made up of a long chain of components called nucleotides 

The chemical structure of RNA is very similar to that of DNA , with twodifferences: (a) RNA contains the sugar ribose, while DNA contains the

slightly different sugar deoxyribose (a type of ribose that lacks oneoxygen atom), and (b) RNA has the nucleobase uracil while DNA containsthymine. Uracil and thymine have similar base-pairingproperties.

 most RNA molecules are single-stranded

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GENOME In modern molecular biology and genetics, the genome is the entirety 

of an organism's hereditary information. It is encoded eitherin DNA or, for many types of virus, in RN A . The genome includes boththe genes and the non-coding sequences of the DNA/RNA 

 An analogy to the human genome stored on DNA is that of instructionsstored in a book: The book (genome) would contain 23 chapters (chromosomes); each chapter contains 48 to 250 million letters (A,C,G,T) without

spaces; Hence, the book contains over 3.2 billion letters total;

The book fits into a cell nucleus the size of a pinpoint;  At least one copy of the book (all 23 chapters) is contained in most cells

of our body. The only exception in humans is found in mature redblood cells which become enucleated during development andtherefore lack a genome.

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Non coding DNA  Noncoding DNA describes components of an

organism's DNA sequences that do not encode for protein sequences.

Much of this DNA has no known biological function and at one time

 was sometimes referred to as " junk DNA “. 

Many types of noncoding DNA sequences do have known biologicalfunctions, including the transcriptional and translational regulation of protein-coding sequences.

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 Three prime untranslated region

The three prime untranslated region (3' UTR) is a particularsection of messenger RNA (mRNA). It follows the coding region.

Several regulatory sequences are found in the 3' UTR:  A polyadenylation signal, usually  AAUAAA, or a slight variant.

This marks the site of cleavage of the transcript approximately 30 base pairs past the signal, followed by the addition of severalhundred adenine residues (poly-A tail).

Binding sites for proteins, that may affect the mRNA's stability orlocation in the cell, like SECIS elements (which direct the

ribosome to translate the codon UGA asselenocysteines ratherthan as a stop codon), or AU-rich elements (AREs), stretchesconsisting of mainly adenine and uracil nucleotides (which caneither stabilize or destabilize the mRNA depending on theprotein bound to it).

Binding sites for miRNAs, a type of RNAi.

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Multiple Sequence Alignment  A multiple sequence alignment (MSA) is a sequence alignment of 

three or more biological sequences, generally protein, DNA , or RNA .

Multiple sequence alignment is also an important step for phylogenetic

analysis, which aims to model the substitutions that have occured overevolution and derive the evolutionary relationships between sequences.

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ClustalW ClustalW is a tool to align three or more sequences together in a

computationally efficient manner.

 Aligning multiple sequences highlights areas of similarity which may 

be associated with specific features that have been more highly conserved than other regions

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How it is done?Mi Discoverer

Input sequence

Perform Alignment

 Alignment result

Search similar mi RNA 

mi RNA Discription

Save results

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Input sequence is of RNA consisting of A G C U.

 A human RNA sequence was submitted to find the

miRNA, the CLUSTALW program gives the output intwo files, one is .aln and other is .dnd file.

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RNA INTERFERENCE

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