[EMBOSS] using emma: where to put clustalw

[Robin Colgrove]

Thanks to all for suggestions.
Just putting clustalw in /usr/local/bin did the trick.

Now, I need to figure out why emma/clustalw is giving me such bad 
alignments.
Since I only had 4 sequences, I ended up aligning them pairwise with 
needle, then pieced together the full alignment in vi, but this is not 
going to fly as the number of sequences increases. The online tool I 
use for quick alignments ( 
http://prodes.toulouse.inra.fr/multalin/multalin.html ) does fine, but 
the same fasta file sent either to emma or directly to clustalw gives 
obviously wrong alignments, even though the nucleotide sequences are 
highly homologous.

thanks again

robin



On Apr 12, 2005, at 10:17 AM, Robin Colgrove wrote:

>
> Hello.
>
> I was trying to use emma for a multiple sequence alignment of dna 
> sequencing reads, but it complained that it could not find clustalw. I 
> could not find any mention of clustalw on the EMBOSS page, so I got a 
> copy from the clustalw homepage and -not knowing where to place it- 
> tried the /usr/local/share/ EMBOSS/acd directory. That didn't work, 
> and emma gives the error:
>
>    EMBOSS An error in ajsys.c at line 398:
> cannot find program 'clustalw'
>
> Looking in the emma.acd and ajsys.c files, I can't find any guidance.
>
> Does anyone know how this is supposed to work?
> Alternatively, is there another good way to do multiple sequence 
> alignment?
> Looking ahead, I do not find any obvious way to do contig assembly, a 
> la Phrap, or CAP.
>
> thanks
>
> robin colgrove
>