The document describes a study that aimed to predict non-coding RNAs (ncRNAs) in clinically important Mycoplasma species through comparative genomic analysis. The approach involved extracting intergenic regions from Mycoplasma genomes, searching for sequence similarity across related organisms, parsing alignments using certain cutoffs, and using the parsed alignments as input for the QRNA program to predict putative ncRNAs. Several ncRNAs were predicted for each organism and some showed similarity to known bacterial and eukaryotic ncRNAs.

1. NON-CODING RNA PREDICTION OF CLINICALLY IMPORTANT MYCOPLASMA BY COMPARATIVE GENOMIC ANALYSIS Dissertation submitted to the Madurai Kamaraj University in partial fulfillment for the requirement of Masters of Science in Biotechnology Regn. No:A242009 School of Biotechnology Madurai Kamaraj University Madurai

4. OUTLINE INTERGENIC REGIONS OF ORGANISM OF INTEREST ↓ SEARCH FOR HOMOLOGY ACROSS RELEATED ORGANISMS ↓ PARSE THE ALIGNMENTS WITH CERTAIN CUTOFFS ↓ THE ALIGNMENTS WERE GIVEN AS INPUT FOR THE QRNA ↓ PUTATIVE ncRNA blastn Perl scripts

5. PROTEIN CODING REGION ->INTERGENIC REGION .ptt file ↓ Co-ordinates of protein coding regions ↓ Intergenic region co-ordinates ↓ Intergenic region co-ordinates difference > 50 nucleotides ↓ Range file ↓ Intergenic sequence extraction by EMBOSS application extractseq –regions @rangefile -separate

6. GENOME LENGTH COMPARISION OF THE MYCOPLASMA M.gen- Mycoplasma genetalium M.pne- Mycoplasma pneumoniae M.pul- Mycoplasma pulmonis M.gal- Mycoplasma gallisepticum M.myc- Mycoplasma mycoides M.pen- Mycoplasma penetrans 9,63,879 M.pulmonis 8,16,394 M.pneumoniae 13,58,633 M.penetrans 12,11,703 M.mycoides 580,074 M.genitalium 9,96,422 M.gallisepticum Genome size Organism

7. MYCOPLASMA GENOME – INTERGENIC REGION BAR GRAPH SHOWING THE PERCENTAGE OF INTERGENIC REGION IN THE GENOME OF MYCOPLASMA

17. No. of blastn hits selected for qrna input GRAPH SHOWING NUMBER OF ALIGNMENTS SELECTED FOR QRNA INPUT FOR EACH GENOME THROUGH THE PERLSCRIPT 560263 430551 154026 360830 44433 53927 No. of alignments

21. Number of ncRNA predicted for each organism No. of ncRNAs predicted

22. PICTURE SHOWING THE LENGTH RANGE OF NON-CODING RNAs. (Vertical bars represent the spread of scores and horizontal bar represent the average) Length Range of Non-coding RNA predicted

29. ACKNOWLEDGMENTS Dr. Z. A. Rafi Dr. S. Krishnaswamy The Whole SBT family Ministry of Human Recourses Development Department of Education Department of Science and Technology Department of Biotechnology All my classmates