Home modified by cczhong

cczhong — Mon, 23 Nov 2015 20:06:27 -0000

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-Welcome to your wiki!
+#
+#  HMM-GRASPx: guided search and assembly of short peptides using HMM models
+#
+#  Please direct comments, suggestions, bug-reports to Cuncong Zhong (czhong@jcvi.org)
+#

-This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].
+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'.

-The wiki uses [Markdown](/p/hmm-graspx/wiki/markdown_syntax/) syntax.
+   * '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.

-[[members limit=20]]
-[[download_button]]
+   * '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'

Home modified by cczhong

cczhong — Fri, 20 Nov 2015 23:53:21 -0000

Welcome to your wiki!

This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].

The wiki uses Markdown syntax.

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Home modified by cczhong

Home modified by cczhong

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