Description:

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 by FPC.

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.

Usage:

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 sativa" /home/downloads/daily/nc0903.flat

size2band < path to standards file > < < file having names of .sizes files >
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