FASTA Splitter

Executables are provided to split your FASTA file into several smaller ones.
This may be needed to produce files obeying the maximum sequence number for external services as TMHMM.
The FASTA splitter we currently provide is written by David Mathog, Biology Division, Caltech.
The original up-to-date source can be downloaded from the original site. Below, we provide the source and the executables we compiled from this source.

To split a FastA file of 10.000 sequences into 5 files with 2000 sequences each without changing the order of the sequences use:

fastasplitn fastafile 5 0 2000, where "fastafile" is the name of your FastA file.

Please note that:

• this program has to be run from the command line;
• output will be written to files starting with frag, and that existing "frag" files will be overwritten without notifying you;

Source and binaries can be downloaded here (for Linux/Mac binaries do not forget chmod u+x):
C-source
Windows executable
Linux (i686) binary
Mac OS X universal binary (tested on PPC, OS-X 10.4.11).

Combining output in a single file

Output files can be combined in a single file with several utilities. We indicate:

• You can use cat on Unix-based systems (incl. Mac OS X). To combine all files ending in tmhmm.out, for example, use:
  cat *tmhmm.html > all_tmhmm.html or cat GPI*.txt > GPIall.txt
• On Windows you could run from the command prompt:
  • use type: type *tmhmm.htm > all_tmhmm.htm or type GPI*.txt > GPIall.txt
  • use copy as indicated by Microsoft:
    "Combining files:
    If you specify more than one Source, separating entries with a plus sign (+), copy combines the files into a single file. If you use wildcard characters (that is, * or ?) in Source, but you specify a single file name in Destination, copy combines all files matching the file name in Source and creates a single file with the file name specified in Destination. In either case, copy assumes the combined files are ASCII files unless you use /b."
  • Or download and install GNU Coreutils, which includes the cat command. Or download another "combine" utility.