Alignment Help

[Mark D'Ascenzo]

Martin Chan wrote:

> Hi netters,
>    I use BLAST to search for dbEST in GenBank against my cDNA clone and
> a hundred hits pop up. Are there any ways I can save all the nucleotide
> sequences (preferably in FASTA format) result efficiently?

I've found that the easiest way is to parse out the Genbank IDs and then
retrieve the sequences using Batch Entrez:

http://www.ncbi.nlm.nih.gov:80/Entrez/batch.html

>
> Just one more, are there any multiple alignment freewares that can
> perform multiple alignment of  more than 100 DNA sequences efficiently?
> I have tried BioEdit, but the outcome is unsatisfactory.

On unix: ClustalW works quite well for this:

http://www-igbmc.u-strasbg.fr/BioInfo/ClustalW/

Regards,

Mark