Analysis of microbial genomes and their applications

Dr. Deepak Malik Deptt. of Biotechnology U.I.E.T, K.U.K

Introduction Genomics a) Structural genomics b) Functional genomics Shot gun sequencing method for sequencing genomes
Steps of this method are
1) 2) 3) 4) 5) 6)
Isolation of bacterial chromosomal / plasmid DNA RE digestion to obtain a collection of fragment with overlapping sequence Construction of genomic library Sequencing of inserted DNA fragment of each clone Analysis of all sequences by DNA sequencer Final assembly of bacterial genome in auto assembler by using software

Genomics Software


Alscript by Barton GroupProgram to format multiple sequence alignments by Geof Barton group. Amplify Amplify is a freeware Macintosh program for simulating and testing polymerase chain reactions (PCRs). Biocatalogue EBI software directory of general interest in molecular biology and genetics. Bioexplorer Toolbar An easy toolbar for NCBI databases BioJava Biological module for Java programming language. BioPAX Develop a common exchange format for biological pathways data. Biotech Resource at UNM.edu Free Software that is Relevant to the Molecular Biology and Structural Biology BioPerl BioPerl: biological module for Perl programming language. BioPHP BioPHP: biological module for PHP programming language. BioPython BioPython: biological module for Python programming language. BioRuby BioRuby: biological module for Ruby programming language BLAST at NCBI Blast public domain software served by NCBI of USA. BoxShade Pretty Printing and Shading of Multiple-Alignment files from http://www.ch.embnet.org/ Cn3D Application that allows to view 3D structures, at NCBI, NIH, USA. CLC Bio Basic bioinformatics analyses and data management - free download DomainParser A protein domain partition program EMBOSS EMBOSS is a package of free open source software for bioinformatic analyses E-cell Simulating intracellular molecular processes of living cells project eXtropia Several free web tools Genamics Genamics SoftwareSeek is a respository and database of freely-distributable and commercial tools for use in molecular biology GeneDoc Multiple sequence alignment editor, analyzer & shading utility for windows Genesis Information about GEneral NEural SImulation System GNU Free software foundation - several opensource programming tools for free OS such as LINUX.HMMER HMMER: Hidden Markov models for biological sequence analysis by Sean Eddy. NIH Image Image analysis program for Macintosh from NIH MassARRAY RT Software (Sequenom) MatInspector Detection of transcription factor binding sites Matt's Script Archive Several free Perl scripts MB Shotcuts List of several free molecular biology softwares

Application of microbial genomics

1) Comparative genomics revealed that genome size vary considerably. Mycoplasma genitalium- ( 5.8x105 bp) Bacillus megaterium- (3x107 bp) 2) Vibrio cholerae have two or more chromosomes 3) E.coli has around 600 operand 4) Frequenting of paralogues ranging from 26% to 75% 5) Pseudogenes occur in prokaryotic genomes 6) Some bacterial spp. have more genes than lower eukaryotes 7) Several yeast genes have homologues among the human genes of unknown function 8) Genome of achaea have similarities with eukaryotic genomes 9) (113 to 233) human genes have directly transferred from bacteria into human genome 10) Comparison of sequence permit identification of min set of genes required to sustain life 11) Developing molecular phylogeny

 References

Oligonucleotide hybridizations on glass supports: a novel linker for oligonucleotide synthesis and hybridization properties of oligonucleotides synthesised in situ.". Nucleic Acids Res. (Maskos U, Southern EM.) 20 (7): 167984. 11 Apr 1992. Augenlicht and Kobrin (1982). Cancer Research 42: 10881093. Augenlicht et al. (1987). Cancer Research 47: 60176021. Augenlicht et al. (1991). Proceedings National Academy of Sciences 88: 32863289. Kulesh DA, Clive DR, Zarlenga DS, Greene JJ (1987). "Identification of interferon-modulated proliferation-related cDNA sequences". Proc Natl Acad Sci USA 84 (23): 84538457. Schena M, Shalon D, Davis RW, Brown PO (1995). "Quantitative monitoring of gene expression patterns with a complementary DNA microarray". Science 270 (5235): 467470. Lashkari DA, DeRisi JL, McCusker JH, Namath AF, Gentile C, Hwang SY, Brown PO, Davis RW (1997). "Yeast microarrays for genome wide parallel genetic and gene expression analysis". Proc Natl Acad Sci USA 94 (24): 1305713062.

Thank you