NAME

     just30 - cut all but first 30 bases of a DNA sequence

SYNOPSIS

     just30  filename ...

DESCRIPTION

     Just30 is a very simple program that reads in DNA  sequences
     and  only  writes  out  the  first 30 bases of each sequence
     found.  The aim of the program is to make it  easy  to  dis-
     cover  unknown sequencing vectors that are contaminating the
     early parts of DNA sequence reads.  By removing all  regions
     of   sequence   that  are  unlikely  to  contain  artificial
     sequences, it is possible to increase the sensitivity of the
     sequence   comparisons   without  being  swamped  by  random
     matches.   The  sequences  output  by  just30  have  to   be
     clustered  by  some other program such as N2tool to discover
     which ones are likely to be contaminated.

     Sequences can be spread amongst any number of files.   Vari-
     ous  sequence formats are supported including GenBank, EMBL,
     plain, (unformatted sequence files),Staden's semi-colon  and
     Experiment file formats, and also 2 NBRF/FASTA style formats
     with the description either on the same line as  '>sequence-
     name'  or  with the description on the line immediately fol-
     lowing the sequence name.

USAGE

  just30 filename1 filename2 filenameN
     This flag denotes the start of a  list  of  space  separated
     filenames  which  hold DNA sequence information. No default,
     always required.

SEE ALSO

     N2tool(1), ICAass(1), ICAtool(1), ICAprint(1),  ICAstats(1),
     ICAmatches(1), tofasta(1), ssort(1), just30(1)

BUGS

     I hope its too simple to be buggy ! Should allow  user  con-
     trol of clipped region.