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.

Description

FIELD OF THE INVENTION [0001] The present invention relates to automatic assembly of mRNA sequences from databases containing large numbers of partial cDNA sequences. BACKGROUND OF THE INVENTION [0002] In human cells, genetic material is stored as DNA in a nucleus of the cell. When a certain protein is needed by the cell, a portion of the DNA is transcribed as mRNA, which is transported the cytoplasm of the cell. In the cytoplasm, ribosomes create proteins, using the mRNA as a template. Generally, the mRNA comprises a long sequence of bases, each triplet (codon) of which encodes a specific amino acid. Thus, a sequence of triplets encodes a sequence of amino acids, which form a protein. [0003] Cell function can, theoretically, be analyzed by determining the type of and ratio between the proteins in the cell. However, proteins are very delicate materials, which are difficult to analyze. mRNA, which controls the creation of the proteins, is easier to separate and analyze. Although seve...

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Benefits of technology

[0017] It is an object of some embodiments of the present invention to provide a method of mRNA assembly which reduces existing raw EST databases, removes errors therefrom and facilitates the creation of longer and/or complete mRNA sequences. The desired end result is a reduced database in which each mRNA sequence and/or EST encodes a different

Problems solved by technology

However, proteins are very delicate materials, which are difficult to analyze. mRNA, which controls the creation of the proteins, is easier to separate and analyze.

Second, in the process of transcribing DNA, changes, especially deletions, are made to the nucleotide sequence.

Unfortunately, the art of reading mRNA sequences is not yet completely developed.

The error rate of the reading increases with increasing length of the mRNA sequence.

The common errors are insertion or deletion of bases, and errors in the identification of individual bases.

At a certain sequence length, the error rate increases to a point where further reading is not possible.

In addition, EST databases contain many other types of errors, which may be accumulated during the complicated process of EST generation in addition to features, inherent in the mRNA, which make the assembly difficult.

These causes of difficulty include:

However, since t

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