FSD2 is a command line version of FSD and it requires executing
the perl script fsd2.pl. fsd2.pl reads an incremental update file
downloaded from GenBank and creates individual files containing
GenBank records. It also creates the Bands and Sizes files needed
GenBank posts the incremental update file every morning at around
6 at the following ftp location: ftp://ncbi.nlm.nih.gov/genbank/daily-nc/.
fsd2.pl scans through this file looking for the organism that you
specify on the command line. If a match is found and the sequence
length is > 40,000 bp, the corresponding GenBank record is written
to a new file.
fsd2.pl uses sequence data from the above GenBank record and cuts
them according to a specified restriction digest enzyme (HindIII
is the default enzyme). The restriction enzyme would have to be
changed manually in fsd2.pl in case a different enzyme has to be
used.The size of each fragment is determined in order to be used
later on. A script named size2band is called next which generates
bands from the sizes determined above. Usage Description for size2band
is provided later in the document.
The resulting .bands and .sizes files created are moved to the fpc
directory by fsd2.pl. The .bands files have the following naming
format: xxxxxxsd.bands, where the "xxxxxx" portion is the GenBank
accession number. The .sizes files are named as yyyymmdd.sizes where
"yyyymmdd" is the current date. All the computationally created
clones are referred to as the Simulated Digest(SD) Clones. They
have the following naming format: xxxxxxsd1 where "xxxxxx" is the
GenBank accession number.
fsd2.pl does subcloning so that the clones generated from a sequence
are not too long. Any clone having more than 55 bands is a candidate
for subcloning. Subclones are named similar to the above SD clones,
only difference is that they have incremental digits as prefixes.
For eg: xxxxxxsd1, xxxxxxsd2 etc.
fsd2.pl < dir for creating genbank records > < fpc_path > "< organism
name >" < genbank update file >
Note: Organism name needs to be enclosed in double quotes("")
Eg: fsd2.pl /home/downloads/daily/rice /home/fpc/rice/OSJNB "Oryza
size2band < path to standards file > < < file having names of .sizes
Note: The standards file is the standard marker file used in Image.
A sample file will be provided with this package.
Eg: size2band /home/imdata/lambdahilo.std < sizes_list.txt