Alignment Help

Mark D'Ascenzo mdd9 at cornell.edu
Thu May 18 19:54:04 EST 2000

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:


> 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:




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