Manually correcting Alignments

As the tRNA example above demonstrates, sequence alignments are often unsuitable as a basis for determining consensus structures. As a last resort, one may always try manually correcting an alignment. Sequence editors that are structure-aware may help in this task. In particular the SARSE http://http://sarse.kvl.dk/ editor, and the ralee-mode for emacs http://personalpages.manchester.ac.uk/staff/sam.griffiths-jones/software/ralee/ are useful. After downloading the ralee-files extract them an put them in a folder called ~/Tutorial/Progs/ralee. Now either read the 00README file or simply copy the .emacs file from the Tutorial/Data-folder in your home directory (~/.), open it and replace the filepath with path to your elisp-directory (should be ~/Tutorial/Progs/ralee/elisp.

Next try correcting the ClustalW generated alignment (four.aln) from the example above. For this we first have to convert it to the Stockholm format. Fortunately the formats are similar. Make a copy of the file add the correct header line and the consensus structure from RNAalifold:

  $ cp four.aln four.stk
  $ emacs four.stk
  .....
  $ cat four.stk

The final alignment should look like:

# STOCKHOLM 1.0

K00349          --GCCGAAAUAGCUCAGUUGGG-AGAGCGUUAGACUGAAGAUCUAAAGGUCCCCGGUUCAAUCCCGGGUUUCGGCA--
K00283          GGGCCG--GUAGCUCAUUUAGGCAGAGCGUCUGACUCUUAAUCAGACGGUCGCGUGUUCGAAUC--GCGUCCGGCCCA
M10740          --GCGGAUUUAGCUCAGUUGGG-AGAGCGCCAGACUGAAGAUUUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCA--
AF346993        --CAGAGUGUAGCUUAAC---ACAAAGCACCCAACUUACACUUAGGAGAUUUCAACUUAACUUGACCGCUCUGA----
#=GC SS_cons    ..(((((((..((((.........)))).(((((.......))))).....(((((.......))))))))))))...

Now use the functions under the edit menu to improve the alignment, the coloring by structure should help to highlight misaligned positions.