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HMM-GRASPx: guided search and assembly of short peptides using HMM models

Please direct comments, suggestions, bug-reports to Cuncong Zhong (czhong@jcvi.org)

1: Runing individual programs

* 'graspxp-build' is used to construct the index. Assuming that you are under directory
  '/HMMGRASPx_home/', simply type './bin/graspxp-build ./Examples/mix3fams.fa'. The build
  program will create a set of indexing files and put into '/HMMGRASPx_home/WorkSpace'.


* 'graspxp-assemble' is used to perform targeted assembly. Assuming that you are under 
  directory '/HMMGRASPx_home/', and that you have finished the previous building step, 
  simply type 
  './bin/graspxp-assemble ./Examples/mix3fams.hmm ./Examples/mix3fams.fa raw_contigs.fa'.
  The program will generate file 'raw_contigs.fa', which is in the FASTA format and contains
  all contigs being assembled in this stage.


* 'graspxp-map' is used to align the short peptides against the assembled contigs. Assuming
  that you are under directory '/HMMGRASPx_home/', and that you have finished the previous
  assembly step, simply type
  './bin/graspxp-map ./Examples/mix3fams.fa raw_contigs.fa mapping.list'.

  IMPORTANT: Note that this step will directly mapping short peptides against the raw contigs
  generated from the previous step. We suggest that the raw contigs being first verified by
  HMMER3 re-alignment (e.g. between './Examples/mixfams.hmm' and 'raw_contigs.fa') before donig
  the mapping. This step is optional but important in reducing false-positive predictions.
  Below you will find the use of a driver script that automatically include the verification 
  process.

  The resulting mapping output is a table that contains three fields, namely 1: the ID of the
  read in the data set; 2: the header/name of the read; and 3: the header/name of the contig
  where the read is mapped onto.

2: Using the "RunHMMGRASPx.pl" script to streamline your analysis

* The script requires HMMER3 (http://hmmer.janelia.org/). This current release should 
  contain a copy of the software under the '/HMMGRASPx_home/ThirdParty' folder.
* You need to compile HMMER3. First go to '/HMMGRASPx_home/ThirdParty/hmmer-3', and
  then type './configure'.
* In the same directory, type './make'. If the compilation is successful, you should
  find that all executables have been put under directory 
  '/HMMGRASPx_home/ThirdParty/hmmer-3/binaries'.


* After compiling HMMER3, you should be able to use the "RunHMMGRASPx.pl" script. To
  analyze the data given in '/HMMGRASPx_home/Examples', simply type (assume you are under
  /HMMGRASPx_home/)
  'perl Scripts/RunHMMGRASPx.pl --hmm=Examples/mix3fams.hmm --seq=Examples/mix3fams.fa --out=TestResults --home=./ --index=WorkSpace/ --param=Settings/param'


* To find out meaning of the options, please type 'perl Scripts/RunHMMGRASPx.pl'