fuzznuc output

[Graziano P.]

Hi,

I have installed the EMBOSS version 2.3.1.
I have made an analisys with the fuzznuc program in this way:

$ fuzznuc
Nucleic acid pattern search
Input sequence(s): mysequence
Search pattern: acgtggac
Number of mismatches [0]: 2
Output report [af049916.fuzznuc]:

The output file is:

$ more  af049916.fuzznuc
 
       AF049916      148 ATGTGGAT
       AF049916      416 ACGTGGGC
       AF049916      845 TCTTGGAC
       AF049916     1722 ACGTGGGC
       AF049916     2007 ACGTGTGC
       AF049916     2257 ACATGTAC
       AF049916     3183 ACGTAAAC
       AF049916     3377 TCGTGGAA
       AF049916     3914 ACGTGCAC
       AF049916     4058 ACATGGAC
       AF049916     4317 ACGTAAAC
       AF049916     4534 TCGTGGAA
       AF049916     4906 ACATGGAA
       AF049916     5877 ACATGGAC
       AF049916     5954 TCCTGGAC
       AF049916     6024 CCCTGGAC
       AF049916     6094 ACGTGGCA
       AF049916     6127 GCCTGGAC
       AF049916     6148 ACATGGAC
       AF049916     6160 TCGTGGAC
       AF049916     6208 ACGTCGAC

As you can see there is no name for each coloumn of the table; moreover this output is different from that you can see in the EMBOSS HELP, i.e. for example:

########################################
# Program: fuzznuc
# Rundate: Thu Apr 11 13:34:06 2002
# Report_file: stdout
########################################

#=======================================
#
# Sequence: HHTETRA     from: 1   to: 1272
# HitCount: 2
#
# Pattern: aagctt
# Mismatch: 0
# Complement: No
#
#=======================================

  Start     End Mismatch Sequence
      1       6        . aagctt
   1267    1272        . aagctt

#---------------------------------------
#---------------------------------------

I have tried to use the option -rformat seqtable, like suggested in the help, but the the program says:
"   EMBOSS An error in ajacd.c at line 11225:
unknown qualifier -rformat"

Have you got any idea about this problem? Is the matter in the EMBOSS version?


Thanks

Graziano


--------------------------------------------------------------------------------------
Graziano Pappadà
areagp61 at yahoo.it
--------------------------------------------------------------------------------------

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