Basic Applied Bioinformatics

CHAPTER 36Genome Annotation in Prokaryotes

CS Mukhopadhyay and RK Choudhary

School of Animal Biotechnology, GADVASU, Ludhiana

36.1 INTRODUCTION

The genomic machinery harbors several signals, elements and conserved regions, namely, promoter signals, transcription start and termination signals (start codon “ATG” and termination codons: Ochre: “TAA”, Amber: “TAG”, Opal: “TGA”), codons, exons, intervening introns (delimited by exon–intron boundaries), etc. Use of suitable software enables the researchers to identify and annotate the various regions of the genome. In this chapter, we will use the GeneMark program to learn gene finding and genome annotation in prokaryotes.

GENEMARK PROGRAM FOR GENE FINDING IN PROKARYOTES

This is a program for ab initio gene prediction of prokaryotes and eukaryotes. The suite of programs available in GeneMark includes the following:

1. Gene prediction in bacteria, archaea, metagenomes and meta‐transcriptomes:
   • GeneMark‐S
   • “GeneMark.hmm with Heuristic models”
   • MetaGeneMark
2. Gene prediction in Eukaryotes:
   • GeneMark‐ES
   • GeneMark.hmm
3. Gene prediction in Transcripts:
   • GeneMarkS
   • “GeneMark.hmm with Heuristic models”
4. Gene prediction in Viruses, Phages and Plasmids:
   • “GeneMark.hmm with Heuristic models”
   • GeneMark‐S

36.2 OBJECTIVE

To annotate the partial genome of a prokaryotic organism, using the GeneMark.hmm (Lukashin and Borodovsky, 1998) online tool.

36.3 PROCEDURE

1. Download the nucleotide sequence from Nucleotide database (NCBI) and save it in Notepad in FASTA format: ...