Documentation read from 04/17/2019 22:07:25 version of /vol/public-pseed/FIGdisk/FIG/bin/svr_cdd_scan.



    svr_cdd_scan [options] < seqs.fa > cdd.table

Scans protein sequences for conserved domain hits in NCBI CD-Database.

Command-Line options


With the -d option, the program uses sequences instead of GI numbers as queries. This can be much slower.

-i ID_list

Comma separated input sequences/IDs .


With the -s option, the short form of output will contain one line for each sequence with 7 columns:

  [ seq_id, specific_hits, superfamiy_hits, multi-domain_hits, 
            names_for_specific_hits, names_for_superfamiy_hits, names_for_multi-domain_hits ]

If there are more than one hits in a column, they will be comma delimited.


The FASTA file containing input sequences is read from STDIN.


The table containing CDD hits is written to STDOUT.

Without the -s option, the output table is -column table that may contain multiple lines for each input sequence:

  [ seq_id query_no query_id hit_type pssm_id
    from to e_value bit_score accession domain
    short_name incomplete_flag superfamily ] 


Hey! The above document had some coding errors, which are explained below:

Around line 65:

You forgot a '=back' before '=head2'