Select 'Manage Pairwise Alignments' and press the 'Proceed' button.

The info dialog will be shown. Press the 'Proceed' button again.

Select the files containing the pairwise alignments which ought to be analysed. You may either choose the file containing the unambiguous, the ambiguous or both EST-mapping results. The files have to be in the PanGEA-BlastN alignment format and multiple files may be selected. Remember, the file containing the unambiguous mapping results is the default PanGEA-BlastN output file.

If you have mapped the ESTs to genes you will get an gene-expression profile like this. The data shown in this example were generated with the sequences published by Torres et al. (2008).

Assuming that you want to identify SNPs, and further assuming that you only want to use alignments from sense-transcripts having a minimum similarity of 98% with the target gene and that at least 90% of the EST should be aligned with the gene. Enter the paramters and press 'Update analysis' button.

Now press the 'Export' button.

Select the pairwise alignments for exporting and than press the 'Export entire subset' button. Choose an output file and press 'Save'. You can use this exported pairwise alignments e.g.: for a subsequent SNP-identification.

Torres TT, Metta M, Ottenwälder B, Schlötterer C.
Gene expression profiling by massively parallel sequencing.
Genome Res. 2008 Jan;18(1):172-7. Epub 2007 Nov 21.