LINEUP allows you to arrange and edit the sequence part of several files simultaneously. Programs like PILEUP, GCLUSTALV and GAP only align using symbol data (the sequence). LINEUP allows you to to align the sequences to reflect structural and functional relationships.
Each sequence is displayed on a separate line. The program works in a similar way to the VAX editor - enter ctrl-Z to get to the command mode. Exit is used to leave LINEUP
LINEUP of what sequence group ? clust.msf
1) You will now create room for a consensus sequence. The command NEW creates an empty file. AUTOCONSENSUS writes the consensus sequence to a new line in the MSF file.
Create a NEW sequence. Enter name (nine letter max): CLUST (the same name as the group)
2) Move the cursor down to an empty line, press return.
3) You are still in the command mode, as the cursor is in the bottom left of the screen, so enter: Autoconsensus
The program writes the consensus sequence to the new line. Any changes made to the other sequences will be reflected in the consensus. NB: The consensus is by character matching, and a majority-decision.
4) Press return. Use the up-down arrows keys to move up one line.
5) Move to position 81 by typing 81 (you won't see it) and press return. (position 33 if using the RNA example).
6) Delete the gap (dot character).
7) Add and delete the dot - watch the consensus sequence change.
8) Return to position 1 (CTRL-H). Enter /LV (/CCAT if editing RNA)
9) Enter / to find the next occurence of LV. You can find any given sequence pattern, using /
10) Make sure that all sequences are the same length if you wish to use PROFILE. Use Ctrl-z and write to save the (edited) files. The consensus sequence is written to a line in the MSF file called CLUST.
11) Try the following commands (after CTRL-Z): ROWMOVE, MOVE, RENAME. REMOVE deletes a fragment, and GET (as in SEQED) reads in a new fragment.
EXIT when finished.