RNAML Report-Semantic Computing and Bioinformatics-Handout, Exercises for Semantics of Programming Languages
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RNAML Report-Semantic Computing and Bioinformatics-Handout, Exercises for Semantics of Programming Languages

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In this handout Sir Sanjay Mishra discussed following points related Semantic Computing and Bioinformatics course at Acharya Nagarjuna University: RNA, Markup, Language, Interference, Technology, RNAML, XML, Schema, Sequence, Deficiencies, Enzymes, Genome
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RNAML

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Contents 1. Brief Introduction of RNA ...................................................................................................... 4

2. RNAML – XML Schema ........................................................................................................ 5

3. Critical Analysis of XML Schema .......................................................................................... 6

3.1.RNA enzymes .................................................................................................................... 6

3.3.RNA Genomes .................................................................................................................. 9

3.4.RNA Mutations ............................................................................................................... 10

4. XML Tree .............................................................................................................................. 11

5. Modifications( In Progress) ................................................................................................... 12

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Table of figures

Figure 1:Venn diagram of RNA ..................................................................................................... 4

Figure 3: A tree Diagram of XML Schema showing various elements and attributes ................... 5

Figure 2: XML schema of RNAML ............................................................................................... 5

Figure 4: RNA enzymes.................................................................................................................. 6

Figure 5: Snapshot of database ....................................................................................................... 7

Figure 6: XML spy view of RNA enzymes .................................................................................... 7

Figure 7: Snapshot of RNA families database ................................................................................ 8

Figure 8: XML spy view of RNA families ..................................................................................... 8

Figure 9: Database of Rfam ............................................................................................................ 9

Figure 10: An instance of Genome ................................................................................................. 9

Figure 11: XML spy view of RNA genome ................................................................................. 10

Figure 12: XML spy view of mutaion ......................................................................................... 11

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RNA Markup Language

1. Brief Introduction of RNA

RNA stands for Ribonucleic Acid, and is one of major cell components involved in gene

expression. Until 1950’s its function was confined only to gene expression. Howver with tha

passage of time, in late 1970’s a pool of various RNA molecules had been discovered with a

myriad fucntions ranginf from catalytic activity to RNA interference technology, covering the

major domains of life( eukaryota, archaea, eubacteria).

Figure 1:Venn diagram of RNA

mRNA, tRNA,

rRNA, tmRNA,

SRP RNA etc

Protein Synthesis

snRNA, snoRNA, SmY,

scaRNA,gRNA,RNase P,

RNase

MRP,YRNA,Telomerase

RNA etc

Post-translational

Modification or DNA

Replication aRNA, crRNA, long

ncRNA, miRNA,

piRNA, siRNA,

tasiRNA,rasiRNA,7SK

etc

Regulatory RNAs

Regulatory RNAs

Retr transposon, Viral

Genome, Viroid,

Satellite RNA etc

Parasitic RNAs

Parasitic RNAs

Viruses, Bacteria

strains

RNA genomes

HDV

Ribozyme,VS

Ribozyme, CoTC

Ribozyme etc

Ribozymes RNA Families

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2. RNAML – XML Schema

Allison Waugh, constituted a Dcoument Type Definition(DTD) and XML Schema in 2002, so as

to enable easy exchange of RNA data on RNA sequence and information within RNA

community. The syntax enabled easy exchange of data on sequences and structures of RNA

molecules.

Figure 3: A tree Diagram of XML Schema showing various elements and attributes

Figure 2: XML schema of RNAML

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3. Critical Analysis of XML Schema

Upon thorough analysis of XML schema, it was seen that it fulfilled queries on sequence/

Structure retrieval of RNA molecules as well as the organism.

However, as per our understanding it had the following deficiencies:

1. RNA enzymes 2. RNA Families 3. RNA Genome 4. Mutations

3.1. RNA enzymes

Discussion

Several RNA molecules act as RNA enzymes, Ribozymes. Modomics Database -is a

repository of Ribozymes. It was established by Horkawicz et al in 2006, and contains

information for RNA enzymes in the following data fields such as Full Name, Enzyme

Type, Catalytic Domain, UniProtID, Orf, and GI. [1]

The existing version of XML Schema lacks suitable structure to incorporate the above

information, due to which any information regarding RNA Enzymes cannot be retrieved/

accessed from the present schema structure of RNAML. Hence, there arises a need to

modify the Schema in such a way that information regarding RNA Enzymes can be

shared within RNA community.

Figure 4: RNA enzymes

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Figure 5: Snapshot of database

Figure 6: XML spy view of RNA enzymes

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3.2. RNA Families

Discussion

RNA families have been categorized into RNA families based upon evolution from

common ancestor in Rfam database. [2]

Each RNA family is represented by multiple

sequence alignments,consensus secondary structuresand covariance models

(CMs).Information regarding RNA families have been incorporated into the following

fields such as Type, Seed, Full, Average length, Sequence Identity, Description in

database; a snapshot of which is given below:

The current version of RNAML schema does not support the information about RNA

families.So, it is vital to modify the Schema structure in such a way that any information

about RNA families is accessable from RNAML XML Schema.

Figure 7: Snapshot of RNA families database

Figure 8: XML spy view of RNA families

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3.3. RNA Genomes

Discussion

Several organisms such as bacteria, viruses have RNA as their genomic content. Rfam

database has a record of 1723 RNA genomes.Each record has details of Kingdom, no: of

RaNA families, no: of regions, Genomic Length, and No: of genomic elements.

These pieces of information are not supporetd by existing RNAML schema structure, and

hence there arises a need to make suitable alterations in RNAML schema such that

information about RNA genomes can be accessed vis RNAML in RNA community.

Figure 9: Database of Rfam

Figure 10: An instance of Genome

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Figure 11: XML spy view of RNA genome

3.4. RNA Mutations

Discussion

This is the main resources page for the RNAML syntax for exchanging RNA

information. This syntax was designed to easily express data on RNA sequence and

structure, and to allow the transmission of information among the RNA community

RNAML Schema supports exchanging of RNA information related to RNA sequence,

sequence annotaion, RNA structure as well as structure annotaion. However, the sequnce

is prone to changes called mutations. These mutations are many a times detrimental to

organism and at times cause no hamr to organism. Information regarding the base at

which mutaion has occurred is not supported by RNAML schema structure. Hence,

addtions need to be made in order to make it complete enough for exchange of any

information on mutations.

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Figure 12: XML spy view of mutaion

4. XML Tree

Fig 2 The

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above figure shows a few elements of XML tree with contributions highlighted in gray.

5. Modifications( In Progress)

1. RNA motifs ( secondary and tertiary structures) 2. RNA Modification pathways 3. Poly A-sites 4. Ribiosomal RNA Mutation databaes(RIDOM)

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References Dunin-Horkawicz S, Czerwoniec A, Gajda MJ, Feder M, Grosjean H, Bujnicki

JM.

MODOMICS: a database of RNA modification pathways.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D145-9.

 Rfam: an RNA family database.Griffiths-Jones S, Bateman A, Marshall M, Khanna A and Eddy SR Nucleic acids research 2003;31;1;439-41PUBMED:

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