[Bioperl-l] Problems running blast

James Wasmuth james.wasmuth at ed.ac.uk
Fri Feb 6 05:36:42 EST 2004

input can be:
    * sequence object
    * array ref of sequence objects
    * filename of file containing fasta formatted sequences

best bet is create a Seq object.  From the HOWTO:

use IO::String;
        use Bio::SeqIO;

        # get a string into $string somehow, with its format in 
        # $format, say from a web form
        my $stringfh = new IO::String($string);
        my $seqio = new Bio::SeqIO(-fh => $stringfh,
                                   -format => $format);

        while( my $seq = $seqio->next_seq ) {
             # process each seq


Hong Ching Lee wrote:

>Hey everyone,
>I have a question about whether i can run remote blast using just a string
>or whether i have to make it into a fasta format file. Can anyone help me
>with this?
>Thank You,
>Bioperl-l mailing list
>Bioperl-l at portal.open-bio.org

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