clustalw2 output format

Question

[prostoesh]

Hey, I'm using clustalw to align protein sequences and I'm having an output like this:

CLUSTAL 2.1 multiple sequence alignment

KIL98380.1                          ----------------------------------------------MNKN
gi|495892927|ref|WP_008617506.      ----------------------------------------------MNKN
gi|83311888|ref|YP_422152.1|        

KIL98380.1                          DLVTAVAGAAGLSKADAAKAVDGVFEAITSALKGGDEVRLVGFGTFAVAS
gi|495892927|ref|WP_008617506.      DLVTAVAGAAGLSKADAAKAVDGVFEAITSALKGGDEVRLVGFGTFAVAS
gi|83311888|ref|YP_422152.1|        DLVTAVAGAAGLSKADAAKAVDGVFEAITSALKGGDEVRLVGFGTFAVAS


KIL98380.1                          RAASEGRNPRTGEKIKIPASKQPKFKAGKGLKDGIQ-
gi|495892927|ref|WP_008617506.      RAASEGRNPRTGEKIKIPASKQPKFKAGKGLKDGIQ-
gi|83311888|ref|YP_422152.1|        RAASEGRNPRTGEKISIPASKQPKFKAGKGLKDGIQ-

Is there an option to create output so each protein would be on just one line i.e. without line break?

Answer 1

[Antonio R. Franco]

There is one of the output file in Clustal, that can be imported as a clustal file (obvious, that is, do not use the open function) into a window program named GeneDoc that will allow you to do what you want and many more things

[prostoesh]

i kinda can't afford an extra step like one more program

i'll be creating a lot of alignments

[Antonio R. Franco]

It's your choice. I am experienced in importing the clustal results into GeneDoc, and I love it.

Give a try..