Multiple sequence outputs???

Charles Bailey bailey at genetics.upenn.edu
Wed May 25 15:33:50 EST 1994

In article <1994May25.103412.1 at omrf.uokhsc.edu>, frank at omrf.uokhsc.edu writes:
> We have aligned two groups of sequences with a short overlap using 
> the fragmetn assembly software.  The total consensus length is about
> 500 bp.  The second group of sequences is offset about 300 bp from
> position 1.
> Now we would like to get a printout with identical nucleotides to 
> the consensus shown as a "-" and differences as the actual base.
> We have tried to use pileup but it gives a completely different
> and very poor alignment. Can you make a data file for the program
> PRETTY that includes offset information for each sequence?  Are 
> there alternate strategies to see these differences?

I have modified GelAssemble to produce precisely this type of output, since
we've found it to be the easiest way to locate discrepancies during sequencing.
The modified version implements the command MASKout:

[x,y] MASKout [char] [FileName]  writes aligned output as in PRETTYout,
                                 except that all bases matching the
                                 consensus are replaced with char.

The output looks like this:

Ko-23d     <                                           ~~~~~~~~T~~~.~~~~~ 18    
Ko-22d     >                              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31    
K7csac6    > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68    
Ko-23      < ~~~~~~~~~~~~~~~~~~~~~~~~~~~N~~~~~~~~~~~~~~~~~~~~~~~N~~~.~~~~ 81    
K0-22      > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 270   
7csac6-R6  < ~~~~~~~~~~~~~~~~~~~~~~~~~                                    332   

I've put the patch to GelAssemble.For (GCG/VMS v7.3) up for anonymous ftp; it
can be retrieved from genetics.upenn.edu as the file

If you have any problems or questions, feel free to drop me a line.

                    Charles Bailey

!              Computational Biology and Informatics Laboratory
!         Dept. of Genetics, Univ. of Pennsylvania School of Medicine
!              Philadelphia, PA USA 19104     Tel. (215) 573-3112
!          Internet: bailey at genetics.upenn.edu  (IN

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