Documentation read from 04/17/2019 22:07:26 version of /vol/public-pseed/FIGdisk/FIG/bin/svr_find_fused_genes.



  svr_find_fused_genes [options] [<seqs.fa] >fusion.tbl

Find genes that are homologous to the query genes and prints a list of fusions among them.


  svr_find_fused_genes -peg 'fig|83333.1.peg.784'  

  svr_find_fused_genes < query.fasta > fusions.table

  svr_find_fused_genes  -o hits.fasta  -r report  -t tree.html  < query.fasta  > fusion.table


usage: svr_find_fused_genes [options] [<seqs.fa] >fusion.tbl

       -a   n_processor     - number of processors to use (D = 4)
       -b   database        - database to search against: SEED (D), PSEED, PPSEED, FASTA file name, FIG genome ID
       -i   min_ident       - minimum fraction identity (D = 0.1)
       -u   max_q_uncov     - maximum unmatched query (D = 100)
       -r   report_file     - output file of psiblast report
       -o   output          - output psiblast search hits in fasta       
       -t   html_tree       - output html tree painted with fusion genes
       -l                   - run search locally if a local database is specified
       -peg fid             - query gene ID

Command-Line options

-a n_processor

Number of processors to use (D = 2 locally or 4 remotely)

-b database

Database for psiblast to search against. It can be a FASTA file name, a FIG genome ID, or a string, SEED, PSEED or PPSEED, to indicate one of the preconfigured database of all protein sequences from complete genomes. The default is SEED.

-i min_ident

Minimum fraction identity used in psi-blast search (D = 0.1).


With the -l option, psiblast search is run locally. The database must be a local FASTA file.

-u max_q_uncov

Maximum unmatched query, c-term or n-term (D = 100).

-o output_file

With the -o option, psiblast hits are written to a FASTA file.

-r report_file

Output file name for psiblast records produced as a 11-column table containing:

  [ subject_id, bit_score, e_value,
    subject_length, status,
    fraction_ident, fraction_positive,
    query_uncov_n_term, query_uncov_c_term,
    subject_uncov_n_term, subject_uncov_c_term ]
-t html_tree

With the -t option, a HTML tree is generated with the functional roles of sequences colored and the fused genes highlighted.


The input search profile is a FASTA file read from STDIN or a PEG ID specified with the -peg option.


The set of predicted fused genes is written to STDOUT.

  [ fused_gene_ID, subject_uncov_n_term, subject_uncov_c_term ]