using ClustalW output to BLASTn search against the nucleotide (nr/nt) collections

Question

[zizigolu]

Hello there

Please someone tell me, how I can employ the resulted multiple alignments of ClustalW in BLASTn search against the nucleotide (nr/nt) collections?

Imagine I have this output of ClustalW

CLUSTAL 2.1 multiple sequence alignment


q_[1938_1979].1      ACCTTGAAGCAAGAAAGGGGAAGTGGAGACAAAACTGATTAA 42
t_[1512_1553].2      ACCAAAAAAGAAGAAGGAGGAGATGGAGAAAAAAAAGACAAA 42
                     ***   **  ***** * ***  ****** ****  **  **

Now I want to use this in BLASTn search against the nucleotide (nr/nt) collections. How can I?

Answer 1

[Antonio R. Franco]

Give a look to MView