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multiple alignments

Potter Wickware wick at NETCOM.COM
Thu Mar 17 19:29:33 EST 1994

Isn't it true that when you follow a procedure like this you bias the 
consensus in favor of the ones first entered?  
P Wickware, Oakland, CA

On 17 Mar 1994 brett at borcim.wustl.edu wrote:

> Hello again, I wrote this letter earlier in the day, but never saw it posted,
> so here goes again. Thanks to all the people who responded to my request on
> how to interpret the results of sequence database searches. It seems there
> needs to be more education of us "wet" biologists as to how these things work.
> Now, my next question. I would like to generate a consensus sequence from my
> favorite virus in order to use as a query sequence that might be more useful
> than any single sequence. I use Macs and VMS. I would like to use GCG to align several protein sequences (>100) in
> order to create a consensus sequence. The problem is that a lot of the
> sequences are only partial. I tried to use PILEUP, but it did not handle
> the sequences with internal overlap well. ie:
>     +++++++++
>     ++++++++++++++++++++++++++++++++++++++
>     ++++++++++++
>             ++++++++++
>     +++++++++++++++++++++++++++++++++++++++
>    +++++++++++++++
>                        ++++++++++++++
>  The result was a blank outfile. However, when I used as input the full-length
> sequences, I got a nice alignment back. So, I have been using this alignment as
> a backbone to align sequences using LINEUP. The Zip routine seems to be able
> to correctly place these internal sequences. However, LINEUP can only handle
> 30 sequences. I have been considering making several LINEUP alignments and then
> aligning the consensuses I get from them. Is this a reasonable way to go? I am
> afraid of misrepresenting some columns with this approach.
>   SO, does anyone have any suggestions as to how best to line up all the seqs
> I got? Other programs you would recommend for me?
> brett at borcim.wustl.edu

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