Tool Description References
BLAST It is a search tool, used for DNA or protein sequence search based on identity. [109]
HMMER Homologous protein sequences may be searched from the respective databases using this tool. [110]
Clustal Omega Multiple sequence alignments may be performed using this program. [111]
Sequerome Used for sequence profiling. [112]
ProtParam Used to predict the physico-chemical properties of proteins. [113]
JIGSAW To find genes, and to predict the splicing sites in the selected DNA sequences. [114]
novoSNP Used to find the single nucleotide variation in the DNA sequence. [115]
ORF Finder The putative genes may be subjected to this tool to find Open Reading Frame (ORF). http://www.ncbi.nlm.
PPP Prokaryotic promoter prediction tool used to predict the promoter sequences present up-stream the gene http://bioinformatics.
Virtual Foorprint Whole prokaryotic genome (with one regular pattern) may be analysed using this program along with promoter regions with several regulator patterns. [116]
WebGeSTer This is a database containing sequences of transcription terminator sequences and is used to predict the termination sites of the genes during transcription. [117]
Genscan Used to predict the exon-intron sites in genomic sequences. [118]
Softberry Tools Several tools are specialized in annotation of animal, plant, and bacterial genomes along with the structure and function prediction of RNA and proteins.
Table 1: Selected tools for primary sequence analyses.