Amino acid sequence comparisons have several distinct advantages over nucleotide sequence comparisons, which, at least potentially, lead to a much greater sensitivity. Firstly, because there are 20 amino acids but only four bases, an amino acid match carries with it >4 bits of information as opposed to only two bits for a nucleotide match. Thus, statistical significance can be ascertained for much shorter sequences in protein comparisons than in nucleotide comparisons. Secondly, because of the redundancy of the genetic code, nearly one-third of the bases in coding regions are under a weak (if any) selective pressure and represent noise, which adversely affects the sensitivity of the searches. Thirdly, nucleotide sequence databases are much larger than protein databases because of the vast amounts of non-coding sequences coming out of eukaryotic genome projects, and this further lowers the search sensitivity.


In the molecular biology, sequence analysis tool is one of the powerful tools for the matching of nucleotide or protein sequence from same or various organism. With help of this tool, scientist can find the function of newly sequence genes, predicte newly change of gene members and find evolutionary relationship. It can be helped to imaging the location and function of protein coding and transcription regulation area in genomic DNA. For the calculating sequence similarity, BLAST is one of the most popular tool for that. BLAST can use with various query sequence against different database. PSI BLAST and RPS BLAST also perform matching against sequence profiles(33 McEntyre, Jo 2002)

Trypsin is effective for the protein digestion, trypsin is one of the proteolytic enzyme. In the human body, trypsin produced as inactive form within the pancrease as atrypsinogen. Than this trypsinogen converted into the trypsin in the small intestine. Trypsin is itself a part of the protein and able to digesting itself which know as autolysis. Which is important for the control level of trypsin. Trypsin composed of 220 residues and it is a globular protein of 24 Kda and its have 13 beta strands. In the trypsin structure, found four region of alpha helix and six disulfide bridges.

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