FACIL Files

FACIL quick usage guide
http://www.cmbi.ru.nl/FACIL

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#  MD5 CHECKSUM OF INCLUDED FILES #
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b751f546a5fa0e9d7dead9e65fe1f09b  BLOSUM62
485e020d00f08f19210caecfa0086a61  DejaVuLGCSansMono-Bold.ttf
f3d432ea48b98f44c69373f5b08509c3  example.fna
59b1d1776a13cd10a1457fc562399d99  facil.pl
0ffce2ebb17dddebc29a46846d31406e  hmmfetch
43b6564aa0d3a655957c69f8d8c69aa1  hmmsearch
b0861258c7be9248256f47c044faffc6  Pfam_fs
2591ca45c713144b0ae7ddd25371ca03  Pfam_fs.ssi
fd6e593f632b3c0472a5728cf8e54f9d  RF1.rfo
7b147a1da8e3f6020d19bc8aba390f52  RF2.rfo
ee6d54ca4293b1451c67414ac0c71dde  RF3.rfo


######################
#  BEFORE YOU BEGIN  #
######################
- FACIL is a Perl script, so you will need an installed version of Perl.
  Perl needs the GD graphics library installed, which is necessary for drawing the Genetic Code Logo.
  Change the following line in facil.pl to change the path to Perl:

#!/usr/bin/perl

- R needs to be installed with the randomForest package (we used version 4.5-34)
  Change the following line in facil.pl to change the path to R:

my $path_to_R = "/usr/local/bin/R --slave";

- Check that hmmsearch and hmmfetch are in the correct build for your computer, and that they are executable.
  The 64 bit version from the HMMER v3.0 package (March 2010; http://hmmer.org) is included.


#################
#  USING FACIL  #
#################
- Call FACIL as follows:

perl facil.pl input.fna 'FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG' -o

- Addition of the genetic code to the command line is optional.
  Note the quotes which are necessary to prevent the command line interpretation of *.
  If no genetic code is specified the default is the Standard Code:
  'FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG'

- Addition of -o (for overwrite) is optional.
  If this option is not added, FACIL will not overwrite previous output files with the same name.


#####################
#  TROUBLESHOOTING  #
#####################
- Sometimes you will see the error message:

ERROR: entropy of only 0s

  In this case, it may be that something went wrong with calling hmmfetch. Try running:

./FACIL_v1.0/hmmfetch

  If this gives an error message, then the version of hmmfetch is not suited for your computer.
  We are working on this.


- If you find any other errors or bugs, please let me know and I will try to fix them.


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#  REFERENCE  #
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Dutilh, B.E., Jurgelenaite, R., Szklarczyk, R., van Hijum, S.A.F.T., Harhangi, H.R., Schmid, M., de Wild, B., Francoijs, K.-J., Stunnenberg, H.G., Strous, M., Jetten, M.S.M., Op den Camp, H.J.M. and Huynen, M.A. (2011).
FACIL: fast and accurate genetic code inference and logo
Bioinformatics 27: 1929-1933.
PMID: 21653513
doi: 10.1093/bioinformatics/btr316