The sequence that was generated contains a small amount of vector sequence at the end of the sequence. If there is only a small insert and the whole insert has been sequenced, there may be vector sequence on both ends.
Before you can begin to trim the sequence, you need the vecbase file. This file contains the pZero-2 sequence that was used to generate the library for these sequences. You should download this file to the desktop of your machine. We can select it in a minute.
Select trim vector and you will be presented with the following warning box
Click choose insertion site now, and the next window will open allowing you to choose a vecbase file. Then a window will appear showing you all the sequences that you have selected as possible insertion sites. Currently none are shown because none have been chosen.
Click on the VecBase button to add sequences from the vector database. Make sure that you have downloaded and installed vecbase file in the right location. Choose that file, and then select pZero2 from the list that follows. This is the vector we used to make the library, and all insertions were made in the EcoRV site. Click that site and it will turn green:
Close the windows to return to the sequence views, and then select trim vector again. This time is will put up a display with each sequence and the amount of vector that is to be trimmed off each end.
Click Trim Checked Items and it will remove the vector sequence from the sequences.
Next, we will trim the ends to remove any very bad sequence. As we saw in the previous page there is often poor sequence at the end. Choose Trim Ends from the Sequence menu. Again, you will get a window displaying all the sequences to be trimmed.
Click Trim Checked Items to remove poor sequences
In the next section we will assemble the sequences.