Method and apparatus for mRNA assembly

Abstract

A method of comparing nucleic acid sequences being ESTs included in a first database of sequences and nucleic acid sequences included in a second database of sequences to form groups of sequences from the two databases that all relate to the same gene. For each one or more n-groups of sequences of one of the two databases, associating therewith lists of nucleic acid sequences, each from one of said two databases, each sequence on the list containing the n-groups, and matching sequences on the lists to generate said group.

1 . A method of comparing nucleic acid sequences being ESTs included in a first database of sequences and nucleic acid sequences included in a second database of sequences to form groups of sequences from the two databases that all relate to the same gene, the method comprising: 
 for each one or more n-groups of sequences of one of the two databases:    (One) associating therewith lists of nucleic acid sequences, each from one of said two databases, each sequence on the list containing the n-groups; and    (Two) matching sequences on the lists to generate said group.    
     
     
         2 . A method for obtaining an mRNA sequence having alternative spliced variants from a database of ESTs, comprising: 
 providing a raw database comprising a plurality of ESTs; and    assembling ones of said ESTs into mRNA sequences using the method of  claim 1 , wherein said assembling includes identifying alternative spliced regions.    
     
     
         3 . A method according to  claim 2 , comprising clustering ESTs which have matching segments and wherein said assembly comprising assembling ESTs which are clustered together.  
     
     
         4 . A method according to  claim 2 , comprising correcting errors in said ESTs.  
     
     
         5 . An mRNA sequence determined by the process of  claim 4 .  
     
     
         6 . An mRNA sequence according to  claim 5 , wherein the sequence comprises at least two alternative spliced regions.  
     
     
         7 . An mRNA sequence according to  claim 5 , wherein the sequence comprises at least three alternative spliced regions.  
     
     
         8 . An mRNA sequence according to  claim 5 , wherein the sequence comprises at least four alternative spliced regions.  
     
     
         9 . An mRNA sequence according to  claim 7 , wherein the sequence represents at least two alternative spliced variants of mRNA sequence, each variant utilizing at least one mutually exclusive alternative splice region.  
     
     
         10 . An mRNA sequence according to  claim 7 , wherein the sequence represents at least three alternative spliced variants of mRNA, each variant utilizing at least one mutually exclusive alternative splice region.  
     
     
         11 . An mRNA sequence according to  claim 7 , wherein the sequence represents at least four alternative spliced variants of mRNA, each variant utilizing at least one mutually exclusive alternative splice region.  
     
     
         12 . An mRNA sequence according to  claim 7 , wherein the mRNA sequence is obtained from a single tissue type.  
     
     
         13 . A method of mRNA assembly from a plurality of ESTs, comprising: 
 determining a correspondence between segments in each EST according to the method of  claim 1;  and    generating a directed graph in which each node represents a single segment, and each transition between two nodes represents the existence of an EST in which the two corresponding segments are consecutive.    
     
     
         14 . A method according to  claim 13 , comprising clustering said ESTs into clusters of associated ESTs, wherein said determining a correspondence is performed on individual clusters of ESTs.  
     
     
         15 . A method according to  claim 13 , comprising identifying alternative spliced regions from said graph based on the morphology of the graph.  
     
     
         16 . A method according to  claim 13 , comprising correcting errors in said ESTs based on said graph based on the morphology of the graph.  
     
     
         17 . A method according to  claim 16 , comprising repeating said clustering responsive to said corrected errors.  
     
     
         18 . A method of identifying errors in mRNA sequences, comprising: 
 generating a graph which represents the assembly of segments of ESTs into an mRNA sequence; and    analyzing said graph to determine unusual configurations of said graph.    
     
     
         19 . A method according to  claim 18 , wherein said analyzing comprises identifying multiple end-nodes in said graph.  
     
     
         20 . A method of tuning a database reduction process, comprising: 
 applying the database reduction process, with a certain value for at least one parameter, to a sample database;    determining a reduction ratio in the database; and    reapplying said method with a new value for said at least one parameter if said reduction ratio is not achieved.    
     
     
         21 . A method according to  claim 20 , wherein said at least one parameter comprises the length of n-groups used in matching two ESTs.  
     
     
         22 . A method of EST database processing, comprising: 
 analyzing said ESTs to detect errors;    further processing said ESTs to create mRNA sequences;    determining, responsive to said further processing, corrections for said errors; and    correcting said errors.    
     
     
         23 . A method according to  claim 22 , wherein said further processing comprises assembling said ESTs into mRNA sequences.  
     
     
         24 . A method of designing a DNA chip based on an EST set determined by differential analysis of two biological samples, comprising: 
 reducing said EST set to a set of mRNA sequences;    analyzing said set of mRNA sequences to determine short mRNA sequences which maximally differentiate said mRNA sequences from mRNA sequences found in both biological samples; and    designing a DNA chip which detects said short mRNA sequences.    
     
     
         25 . A method of designing a DNA chip to detect relative expression levels of different variants of mRNA sequences having alternative spliced regions, comprising: 
 reducing an EST database to determine an mRNA sequence having alternative spliced regions;    enumerating short DNA sequences which are only included in the alternative spliced regions of said different variants; and    designing a DNA chip which detects said short DNA sequences.    
     
     
         26 . A DNA chip designed according to the method of  claim 24 .  
     
     
         27 . A method of designing a DNA chip, comprising: 
 indexing an mRNA database to determine the indexing of short DNA sequences in the mRNA database, which short DNA sequences are of a length suitable for detection by a DNA chip;    determining from said indexing a set of short DNA sequences which uniquely identify a desired mRNA sequence; and    designing a DNA chip which detects said set of short DNA sequences.