Rational selection of putative peptides from identified nucleotide or peptide sequences

Abstract

The present invention relates to a method for identifying putative peptides from nucleotides or peptide sequences of unknown function such as both nucleic acid and peptide precursors of a peptide comprising an amidated C-terminal end and, more particularly, to a method wherein putative peptide precursors are identified from a genetic database.

1 . Method for identifying putative peptides of a given function from among nucleotide or peptide sequences of unknown function comprising the following steps: 
 (i) obtaining a polynucleotide or polypeptide database;    (ii) screening said database for the presence of a combination of nucleotides or amino acids indicative of the peptide of given function;    (ii) identifying the polynucleotide or polypeptide sequences which comprise the combination of nucleotides or amino acids indicative of the peptide of given function.    
     
     
         2 . Method for identifying a precursor of a peptide comprising an amidated C-terminal end comprising the following steps: 
 (i) obtaining a polynucleotide or polypeptide database;    (ii) screening said database for the presence of a combination of nucleotides or amino acids indicative of the precursor of the peptide comprising the amidated C-terminal end;    (ii) identifying the polynucleotide or polypeptide sequences which comprise the combination of nucleotides or amino acids indicative of the precursor of the peptide comprising the amidated C-terminal end.    
     
     
         3 . Method according to  claim 2 , characterised in that said database comprises at least one of the polynucleotide sequences and polypeptide sequences corresponding to said polynucleotide sequences.  
     
     
         4 . Method according to  claim 3 , characterised in that said database comprises both polynucleotide sequences and polypeptide sequences corresponding to said polynucleotide sequences.  
     
     
         5 . Method according to  claim 3 , characterised in that said database comprises polynucleotide sequences and accession numbers for said polynucleotide sequences.  
     
     
         6 . Method according to  claim 3 , characterised in that said database comprises polypeptide sequences.  
     
     
         7 . Method according to  claim 4 , characterised in that said polypeptide sequences are obtained by translating the polynucleotide sequences in said database.  
     
     
         8 . Method according to  claim 7 , characterised in that three different polypeptide sequences are obtained, corresponding to translation of three different reading frames of said polynucleotide sequences.  
     
     
         9 . Method according to  claim 3 , characterised in that said database further comprises annotational information relating to said polypeptide or polynucleotide sequences.  
     
     
         10 . Method according to  claim 9 , characterised in that said annotational information comprises at least one piece of information chosen from the origin, the source, the characteristics and the references for said sequences.  
     
     
         11 . Method according to  claim 2 , characterised in that said step of screening said database further comprises the steps of locating the AUG start codon in a polynucleotide sequence and verifying that no stop codon is present between said AUG start codon and the combination of nucleotides indicative of the precursor of the peptide comprising the amidated C-terminal end.  
     
     
         12 . Method according to  claim 2 , further comprising the step, after the step of identifying polynucleotide or polypeptide sequences, of comparing said identified sequences with sequences of known biological function and selecting identified sequences from this group whose biological function is unknown.  
     
     
         13 . Method according to  claim 12 , further comprising the step of comparing the similarity of said selected sequences of unknown biological activity with sequences of known function and, if no similar sequence is found, selecting said sequence of unknown biological activity for further investigation.  
     
     
         14 . Method according to  claim 12 , further comprising the step of comparing the similarity of said selected sequences of unknown biological activity with sequences of known function and, if no similar sequence is found, selection of said sequence of unknown biological activity as a candidate sequence exhibiting the putative function of the known similar sequence.  
     
     
         15 . Method according to  claim 2 , further comprising the step of obtaining the identified polypeptide sequence and evaluation of the properties of said polypeptide sequence.  
     
     
         16 . Method according to  claim 2 , characterised in that said identified polypeptide sequence is H-GQDSIEPVPGQK-NH 2 ; H-YARVQVVA-NH 2 ; H-YFKIDNVKKARVQVVA-NH 2 ; H-PLEPSGG-NH 2 ; H-ELGRGPGPPLPERGA-NH 2 ; or H-YERNRQAAAANPENSRGK-NH 2 .  
     
     
         17 . Method according to  claim 2 , characterised in that the combination of nucleotides comprises the sequence Y1-Y2-Y3-Y4-Y5, in which Y1 is a nucleotide sequence of 1 to 12 nucleotides or is suppressed, Y2 is a codon for Gly, Y3 and Y4 independently are codons for Arg or Lys and Y5 is a nucleotide sequence of 1 to 21 nucleotides or Y5 is suppressed.