Massive Multiple Sequence Alignment tools?

Pascal_Bochet Pascal_Bochet at brown.edu
Sat Apr 27 14:43:01 EST 1996

In article <4lmb4n$905 at swen.emba.uvm.edu>, brianf at med.uvm.edu says...
>Dear Bionet.Software;
>        I am looking for an automated (or even semi-autimated)
>method for generating a multiple sequence alignment of something
>like 6,000 sequences, all of them > 80% identical to one another.
>        I wish to align the envelope gene (or portions there-of)
>which have been sequenced from the Human Immunodeficiency Virus
>type 1 or types 1 and 2.  A BLAST search against the nr dataset
>provided by NCBI reveals that there are several thousand HIV
>env sequences in the database today.
>        If I cannot find a tool already suitable for this, I'd
>like advice on building a program (perhaps using ASN.1 code from
>the NCBI Software Developers Toolkit) that will build a massive
>multiple sequence alignment, given a query sequence (I plan to
>use a "consensus sequence" from an alignment of 50 HIV env genes
>from diverse subtype) and the GenBank/EMBL database.
>        My first thought is to use a tool such as FASTA to
>obtain information about each sequence from GenBank (Is
>it highly similar to HIV env?  If so, what region of it
>aligns with what region of my query) and then use that information
>as a starting point for the multiple sequence alignment.
>        Any thoughts or help will be greatly appreciated. 
>*  Brian Foley               *  btf at t10.lanl.gov                   *
>*  T-10, MS-K710, LANL       *  http://hiv-web.lanl.gov            *
>*  Los Alamos, NM 87545 USA  *  http://www.uvm.edu/~bfoley         *
I remember using a program called Mulblast wich does this kind of things: It 
take the output from blast and puts it in msf format. As all the sequence in 
the blast output are aligned to your test sequence, they will be aligned with 
each other. I am not the author of this program.
Pascal Bochet
Pascal_Bochet at brown.edu
brown university
Providence RI

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