just30 - cut all but first 30 bases of a DNA sequence
just30 filename ...
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.
just30 filename1 filename2 filenameN
This flag denotes the start of a list of space separated
filenames which hold DNA sequence information. No default,
N2tool(1), ICAass(1), ICAtool(1), ICAprint(1), ICAstats(1),
ICAmatches(1), tofasta(1), ssort(1), just30(1)
I hope its too simple to be buggy ! Should allow user con-
trol of clipped region.