6. How can I obtain ESTs for a particular gene model?

EST's which are associated with a particular gene model can be downloaded from within Map Viewer. After you have searched for your gene of interest in Map Viewer and have displayed the desired EST track, clicking on the “Data as Table View” link in the blue sidebar located on the left side of the page will return a tabular report of the data. At the bottom of the report is the “Download Data” link that will enable you to download the table containing the accession numbers of ESTs mapping to the region.

To get the sequence data, the EST accession numbers must be parsed from the table to create a file of EST accessions, one to a line, that can be uploaded for batch download using Batch Entrez:

http://www.ncbi.nlm.nih.gov/entrez/batchentrez.cgi?db=Nucleotide

The EST accessions can be parsed from the table for Batch Entrez using a number of simple methods, including a one-line perl script, e.g.:

perl -nae 'if (/-/){print "$F[2]\n"}' est_table

where the table has been saved as "est_table".

In some cases, it may be necessary for you to adjust the region being shown so that you only download the data in the chromosomal region where your gene is located, and not for all genes in the display.

Another way to do this is to search for your gene in Mapviewer and display the “Gene_seq” map. Next, go to Model Maker by clicking on the “mm” link. Clicking on the “Expand EST” link will display the EST evidence supporting that gene model. Individual sequences can then be downloaded from Entrez Nucleotide after clicking on the accession number for each EST. The limitation to this method is that you can only download one sequence at a time.