Lee H. Pratt

This viewer requires JavaWebStart. You will find a link to Sun to obtain JavaWebStart when you first request this viewer. Details about obtaining JavaWebStart are on the general Instructions page.

Once JavaWebStart has been installed, you can then enter the viewer by launching the application.

The "Step1: Make a Selection" window will appear - please be patient if your internet access is slow. From this window, select the library that contains sequences you want to view. You can, if you wish, also select vector orientation or EST direction (but not both), and either all 96-well blocks of data or only a single block of your choosing. Click on "Get Sequences."

Two new windows appear.  The "Step2:Select a Sequence" window is the one to look at now.  It lists all selected sequences, ordered by sequence name (block number followed by well designation).  Data can be sorted by any other column by clicking on the column header. 
The direction of the sequence read (3' or 5') is shown in the EST column. 
An X in the VF1 or VF2 column indicates that vector is present at the beginning or end of a sequence, respectively. 
TotV indicates that the sequence is entirely vector.
Q16VS is the length of the sequence after trimming away vector, adapter and low quality ends, which is to say as submitted to GenBank.
PolyT is the length of polyT in a 3' EST.  A long PolyT tail is typically associated with a poorer quality sequence.
PID and Method are intended only for internal use for quality control purposes.

To view a sequence in the third, "Display" window, click on the desired sequence in the Select a Sequence window.  You can move quickly up and down the list of sequences using the cursor keys on your keyboard. 
Several options for trimming sequences are available, as is a print function. VScreened = screened for vector + adapter, if any; PolyT = identification of a PolyT region for 3' ESTs; Q16 = sequence trimmed for quality; Q16V =sequence trimmed for quality and vector + adapter if any; Q16VS = sequence trimmed for contaminating sequences as well; Q16VS100 displays that part of the raw sequence that is submitted to GenBank.
The graphical view displays Phred quality scores as a function of sequence position. 
Selecting with a mouse a portion of the sequence identifies it in the graphical view and gives beginning and ending Phred scores. If this selected region is a single base, then it is possible to use the keyboard cursor keys to move the selection, showing the Phred quality score under the graph.
Click on the Print button to print the Display Window.

Clicking on the BLAST button opens a new window. In this new window, click on "Read Sequence." The sequence as trimmed in the Display Window will appear in the Blast Frame window in fasta format. It can be saved to your local computer if desired. "Submit to NCBI" will take you to NCBI's BLAST where you can then use the right-hand button on your mouse (Windows) to enter the sequence as a query at NCBI's BLAST. Alternatively, "Submit to fungen.org" will allow you to do the same on our server (BLAST against sorghum ESTs or Milestone Uniscript Contigs).

If you go back to Window 2 (Select a Sequence), you can also select "Make Fasta." This option allows you to make and save on your local computer fasta files in several formats, reverse complemented or not. You can make them for single sequences or for as many sequences as you like. In the latter case, the shift and control keys (Windows) allows you to select any range of sequences, either between two limits (shift) or individually (control).

The "Failure Report" has no function on this public web site.  This code is used internally to identify the cause of sequencing failures, which is irrelevant here since only sequencing successes are displayed.