Sequence based screening

Abstract

Provided is a method of obtaining a nucleic acid profile of a sample. The method includes creating a DNA library from a plurality of nucleic acid sequences of a mixed population of organisms and sequencing at least one clone in the DNA library. The sequence is compared to a database and identifying sequences in the database which have homology to a clone in the library thereby obtaining a nucleic acid profile of the mixed population of organisms.

What is claimed is:  
     
         1 . A method of obtaining a nucleic acid profile of a sample, comprising: 
 obtaining a plurality of nucleic acid sequences from the sample, wherein the sample comprises a mixed population of organisms;    creating a DNA library from the plurality of nucleic acid sequences;    sequencing at least one clone in the DNA library;    performing a database search using an algorithm to compare the sequence of the at least one clone with the data in the database, wherein the database contains a plurality of nucleic acid sequences from a plurality of organisms; and    identifying sequences in the database which have homology to the at least one clone sequence thereby obtaining a nucleic acid profile of the sample.    
     
     
         2 . The method of  claim 1 , wherein the mixed population of organisms is derived from uncultivated or cultivated microorganisms.  
     
     
         3 . The method of  claim 2 , wherein the uncultivated or cultivated microorganisms are isolated from an environmental sample.  
     
     
         4 . The method of  claim 3 , wherein the microorganisms isolated from the environmental sample are extremophiles.  
     
     
         5 . The method of  claim 4 , wherein the extremophiles are selected from the group consisting of thermophiles, hyperthermophiles, psychrophiles, halophiles, acidophiles, barophiles and psychrotrophs.  
     
     
         6 . The method of  claim 1 , wherein the plurality of nucleic acid sequences are genomic DNA or fragments thereof.  
     
     
         7 . The method of  claim 6 , wherein the genomic DNA, or fragments thereof, comprise one or more operons, or portions thereof.  
     
     
         8 . The method of  claim 7 , wherein the operons, or portions thereof, encodes a complete or partial metabolic pathway.  
     
     
         9 . The method of  claim 1 , wherein the DNA library containing a plurality of clones is selected from the group consisting of phage, plasmids, phagemids, cosmids, phosmids, viral vectors and artificial chromosomes.  
     
     
         10 . The method of  claim 1 , wherein the library is contained in a host cell selected from the group consisting of a bacterium, fungus, plant cell, insect cell and animal cell.  
     
     
         11 . The method of  claim 1 , wherein the sequencing is performed by high throughput sequencing.  
     
     
         12 . The method of  claim 1 , wherein the at least one clone is two or more clones.  
     
     
         13 . The method of  claim 1 , wherein the database is selected from the group consisting of GenBank, PFAM or ProDom.  
     
     
         14 . The method of  claim 1 , wherein the algorithm is selected from the group consisting of Smith-Waterman, Needleman-Wunsch, BLAST, FASTA, BLITZ and PSI-BLAST.  
     
     
         15 . The method of  claim 1 , wherein the homology is defined as a preset threshold.  
     
     
         16 . The method of  claim 1 , wherein the homology is at least about 60%.  
     
     
         17 . The method of  claim 1 , wherein the homology is at least about 70%.  
     
     
         18 . The method of  claim 1 , wherein the homology is at least about 80%.  
     
     
         19 . The method of  claim 1 , wherein the homology is at least about 90%.  
     
     
         20 . A method of obtaining a nucleic acid profile of a sample, comprising: 
 obtaining a plurality of nucleic acid sequences from the sample, wherein the sample comprises a mixed population of plants;    creating a DNA library from the plurality of nucleic acid sequences;    sequencing at least one clone in the DNA library;    performing a database search using an algorithm to compare the sequence of the at least one clone with the data in the database, wherein the database contains a plurality of nucleic acid sequences from a plurality of organisms; and    identifying sequences in the database which have homology to the at least one clone sequence thereby obtaining a nucleic acid profile of the sample.