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

svr_cdd_scan

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

-d

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 .

-s

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.

Input

The FASTA file containing input sequences is read from STDIN.

Output

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 ] 

POD ERRORS

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Around line 65:

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