new moethods

[calvin wang]

I need to use TCOFFE, I understand this is not part of EMBOSS. Is it possible to include new methods in to EMBOSS? how? is there a guide? thanks. 

> Hi, I am new in emboss db config. Need some help in indexing blast db.

This is the long-standing problem of the "new ASN.1 format blast database"

NCBI changed formatdb to create a new index file format, but we have no
documentation on the new format, so we cannot update dbiblast to index it.

We hope to provide the ability to index these blast databases in a future
release, once NCBI release the format specification. I suspect EMBOSS and
FASTA are the only other applications using blast index formats so it is
not an urgent task for them.

Meanwhile, you need to use the 'old' format:

First, you need the original FASTA format file (drosophila.nt)

Then, index it with formatdb but add "-A F" to the command line (to turn
off ASN.1 format).

Hope this helps,

Peter Rice


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