TagSorter 1.1

TagSorter is a database application designed to simplify the collation, sorting, comparison and identification of SAGE tag sequences. Serial Analysis of Gene Expression (SAGE) is a high through put technique for measuring gene expression profiles (Velculescu et al, 1995). It reveals both the identity of transcripts expressed and their relative abundance. It can also be used as a means of gene discovery. Use of SAGE has steadily grown since its invention in 1995 and gene expression profiles have been generated from a variety of tissues and organisms.
A brief overview of the SAGE technique is as follows. Messenger RNA is harvested from the experimental tissue and is converted to double stranded cDNA in such a way that the polyA tail of each message is biotin labeled. This cDNA is digested with the restriction enzyme NlaIII and using the biotin label the 3-most NlaIII digestion products are captured. A BsmFI restriction site adapter is then ligated to these fragments. BsmFI cleaves DNA at a position approximately 14 base pair from its recognition site. This results in short expressed sequence tags (EST) from a defined position within each of the mRNA transcripts present in the original tissue. These fragments are then ligated together to form a concatemer of ESTs which are cloned into a standard plasmid vector and sequenced. Each clone can contain identifying tags for up to sixty mRNA transcripts. Since the relative position of each tag is known and they consist of 10 base pairs of novel sequence, once the NlaIII site is excluded, that uniquely identify the mRNA transcript from which they were generated.
Once an experimental SAGE tag catalogue has been assembled the corresponding mRNA identity of each tag sequence must be determined. NIH has established a SAGE tag database as part of the Cancer Genome Anatomy Project (CGAP) (http://www.ncbi.nlm.nih.gov/SAGE). This provides a convenient look up table that links SAGE tags to mRNA transcripts. The investigator enters a SAGE tag sequence and notes the gene match. Manual entry of sequence into the on line database is time consuming, inefficient and the accuracy of this approach must be called into question through typographical errors introduced during data entry. A better approach is to automate data comparison with the NIH SAGE database and retrieve matches into a fully searchable database for later analysis. We have developed TagSorter to make this possible.
TagSorter consists of seven databases designed to hold the following:
Main - should contain your experimental data
Build - should contain the downloaded NIH SAGE database
ALU - should contain a database of tags known to be in repetitive DNA sequence elements
Library 1 to 4 - should contain further optional SAGE catalogues of your choice with which you wish to compare your experimental data.
TagSorter uses these databases to reveal whether each SAGE tag in your catalogue identifies a known gene or a novel mRNA, identifies whether a SAGE tag is present within a repetitive sequence motif and indicates if the same SAGE tag is present in another SAGE catalogue and also displays the ratio between tag abundances in the two data sets. TagSorter gives you all this within an hour of generating your experimental SAGE catalogue.
Enhancements:
- Fixes a bug which prevented the ratio values for Libraries 1-4 from correctly printing.